Abstract:
The disclosed technology brings histopathology into the operating theatre, to enable real-time intra-operative digital pathology. The disclosed technology utilizes confocal imaging devices image, in the operating theatre, “optical slices” of fresh tissue—without the need to physically slice and otherwise process the resected tissue as required by frozen section analysis (FSA). The disclosed technology, in certain embodiments, includes a simple, operating-table-side digital histology scanner, with the capability of rapidly scanning all outer margins of a tissue sample (e.g., resection lump, removed tissue mass). Using point-scanning microscopy technology, the disclosed technology, in certain embodiments, precisely scans a thin “optical section” of the resected tissue, and sends the digital image to a pathologist rather than the real tissue, thereby providing the pathologist with the opportunity to analyze the tissue intra-operatively. Thus, the disclosed technology provides digital images with similar information content as FSA, but faster and without destroying the tissue sample itself.

Description:
RELATED APPLICATIONS 
       [0001]    This application claims priority to U.S. Provisional Patent Application Ser. No. 62/141,223, entitled Systems and Methods for In-Operating-Theatre Imaging of Fresh Tissue Resected During Surgery for Pathology Assessment by Rachet et al., the content of which is incorporated herein by reference in its entirety. 
     
    
     BACKGROUND OF THE INVENTION 
       [0002]    Solid epithelial cancers account for over 10% of all deaths each year world-wide. This figure is expected to increase. Early-stage cancer diagnosis and subsequent complete surgical removal of the tumor offers the best chance for complete cancer cure. With early-stage tumor screening and diagnostics becoming more efficient, the bottleneck lies in efficient surgical management. Current surgical technology cannot precisely define the margins of a tumor, resulting in missed opportunities for life-saving treatment. Tumor residues may remain undetected and untreated until they grow to advanced stages, at which point both patient death rate and overall treatment costs can dramatically increase. 
         [0003]    The diagnosis of a solid tumor typically involves (i) a screen via a blood test or mucosal smear (molecular diagnostics assays); (ii) gross tumor localization in the body typically by means of radiological imaging (e.g., PET, CT, MRI and ultrasound); and (iii) a visual inspection (e.g., endoscopy), and if necessary, the excision of a tissue sample (e.g., biopsy), and a subsequent pathologic examination. 
         [0004]    The pathology laboratory analysis is crucial in the diagnostic process as it is often the basis for the final diagnosis at which the stage of the tumor is confirmed. The pathologist typically prepares thin tissue sections of a frozen or otherwise fixed tissue sample (e.g., a sample processed with formalin or paraffin) obtained during a diagnostic biopsy, then the pathologist examines the thin tissue sections under a microscope. The morphology of the tissue (e.g., cell size and cell arrangement) is the principal basis for distinguishing between healthy and cancer tissue, and for distinguishing between malignant and benign cancer tissue. 
         [0005]    Because diagnostic techniques and cancer screens are improving, cancers are more frequently detected in the earlier stages. This gives oncology surgeons the opportunity to apply the most efficient and least invasive cancer treatment—complete surgical removal of the tumor. 
         [0006]    If no metastases are present, minimally invasive surgical procedures can be used to remove the solid tumor. Typically, chemotherapy is not necessary for patients who undergo a complete resection of the tumor. However, a complete resection requires “tumor-free margins” of the resected tissue, meaning that no tumor cells are left behind in the patient. 
         [0007]    Currently, there is no reliable means available to guide the resection of solid tumors. For certain indications, this results in the need to re-operate on many patients days after the initial operation when an analysis is obtained from the histo-pathology laboratory. Such follow-up surgical procedures usually lead to less favorable outcomes for the patient, psychological stress, and can roughly double treatment and hospitalization costs. 
         [0008]    Healthcare institutions sometimes perform intra-operative frozen-section analysis (FSA) during certain tumor surgeries. Intra-operative FSA is a pathologic assessment of the resected tissue during ongoing surgeries. In spite of inherent problems, such as inferior sample quality when compared to standard paraffin-embedded histology, possible wrong diagnosis due to freezing artifacts (e.g., fatty tissue, like breast or brain tissue, is not suitable for rapid freezing), and tedious sample preparation (e.g., FSA needs to be planned ahead of surgery), long term studies show that intraoperative FSA can reduce the reoperation rate to 10% in the case of breast tumor resections. 
         [0009]    However, intra-operative FSA requires the prolongation of operation time by at least 30 minutes, which, in addition to inconvenience for the patient and the clinical personnel, results in increased cost of the surgery and complications for operating theatre planning and management. Further, many tumor surgeries today do not include pathologic margin assessment, primarily due to the inconvenience and cost of a frozen section analysis. Thus, there is a need for a system for more efficient in-operating-theatre imaging of tissue. 
       SUMMARY OF THE INVENTION 
       [0010]    The disclosed technology brings histopathology into the operating theatre, to enable real-time intra-operative digital pathology. The disclosed technology utilizes a confocal imaging device that can analyze, in the operating theatre, “optical slices” of fresh tissue without having to fix the resected tissue by freezing and/or processing with formalin or paraffin. This greatly reduces the time necessary for preparing and analyzing a sample and facilitates in-operating-theater analysis of tissue samples obtained during surgery. 
         [0011]    For example, a tissue sample is obtained during surgery and the fresh tissue sample is analyzed by a confocal imaging device located in the operating theatre (e.g., where “operating theatre” includes the area in the operating room, adjacent to the operating room, and/or sufficiently near the operating room such that transport of the sample can be quick and/or does not involve taking the tissue sample out of a sterile environment). The sample is analyzed as a fresh tissue sample (without freezing or other fixation processing that kills cells in the sample), and results are obtained in a timely manner so that feedback is provided to the surgeon while the surgery is still proceeding. For example, images and/or other data obtained from the confocal imaging device can be analyzed remotely by a pathologist (and/or by automated analysis) such that results can be communicated to the surgeon in near real-time. In certain embodiments, the fresh tissue sample is analyzed and results provided to the surgeon within 1 minute of obtaining the sample, within 5 minutes of obtaining the sample, within 10 minutes of obtaining the sample, or within 15 minutes of obtaining the sample. In certain embodiments, the fresh tissue sample has a thickness within a range of 0.5-20 mm, 3-5 mm, 5-10 mm, 7-15 mm, 10-25 mm, 15-30 mm, or 25-35 mm or is no less than 0.2 mm, no less than 0.5 mm, no less than 1 mm, no less than 3 mm, or no less than 5 mm). 
         [0012]    The disclosed technology, in certain embodiments, includes a simple, operating table-side digital histology scanner, with the capability of rapidly scanning all outer margins of a tissue sample (e.g., resection lump, removed tissue mass). Using point-scanning microscopy technology, the disclosed system, in certain embodiments, precisely scans an “optical section” of the resected tissue, and sends the digital image to a pathologist rather than the real tissue, thereby providing the pathologist with the opportunity to analyze the tissue intra-operatively. Thus, the disclosed technology provides digital images with the same information content as FSA, but faster and without destroying the tissue sample itself (e.g., without killing cells). 
         [0013]    For example, a resection lump may be placed into the disclosed histology scanner by an operating theatre nurse and the scanner will rapidly (e.g., in less than 10 minutes) acquire pathology information necessary for an intra-operative pathology consultation. A pathologist can receive and view the digital images remotely and communicate his/her analysis digitally back into the operating theatre to guide the next surgical steps. Further, since the tissue is imaged outside of the patient, it can be stained with one or more of a wide range of fluorescent dyes (e.g., Proflavin, Acridin Orange, and eosin stain). 
         [0014]    The disclosed technology, in some implementations, includes a medical device to assist a surgery group in obtaining a digital image at the microscopy level of a patient sample, for example, a tumorous tissue resected during cancer surgery. The captured image can be used by a pathologist to provide assistance, for example, from a remote location, to the surgery group. For example, the pathologist may evaluate the quality of the surgery from a remote location to ensure that the tumor has been completely removed. In certain embodiments, this review by the pathologist is performed quickly (e.g., in less than 5, 10, 15, or 20 minutes) such that if further removal of the tumor is necessary, the remaining portions of the tumor can be removed during the same operation. 
         [0015]    In some implementations, the device includes a holder to carry the sample and position it on the reader and an imaging system (e.g., a reader) capable of fluorescence microscopy imaging on thick fresh tissue. In some implementations, a computer interface displays the images from the reader to the surgery group. In some implementations, sharing software is used to share images and comments with the pathology group (e.g., outside of the operating theatre). 
         [0016]    In one aspect, the invention is directed to a system for in-operating-theatre imaging of fresh tissue samples resected during surgery (e.g., cancer surgery) for pathology assessment, the system comprising: a light source for providing (e.g., laser or other light source providing light with a wavelength of 488 nm or between 450-490 nm) an illumination beam that illuminates a fluorescent stained, fresh sample (e.g., a fluorescent-stained fresh sample) (e.g., an unsliced sample preserved for definitive assessment in follow-up testing), wherein the fresh sample is held by a sample holder located in an operating theatre; a beam expander (e.g., collimating lens (e.g., for use with a monomode fibered laser) or a telecentric afocal magnification relay (e.g., for use with a collimated laser)) for expanding the waist of the illumination beam to a size comparable to the field of view to be illuminated, thereby providing a collimated illumination beam; a beam splitter (e.g., dichroic mirror/filter, prism, or grating(s)) located between the sample and a detector array, for directing the collimated illumination beam toward a micro optical element array; the micro optical element array (e.g., comprising refractive lenses, Fresnel zone plates, micro reflective objectives, and/or GRIN lenses; e.g., a micro lens array) for focusing the collimated illumination beam from the beam splitter onto the sample, thereby forming an array of tight foci for exciting the fluorescence in the sample to produce the back-emitted light, wherein the micro optical element array is configured such that: the micro optical element array collects back-emitted light from the sample, and the collected back-emitted light propagates (e.g., as individual collimated beams) and is directed (e.g., by a set of optics) to a detector array; and a gap (e.g., an airgap) of less than 500 μm (e.g., 50-150 μm, 80-120 μm) is maintained between the micro optical element array and a transparent window (e.g., glass, quartz, sapphire, plastic) onto which (e.g., above which) the sample is placed for imaging; a scanning stage for moving a position of the micro optical element array relative to the transparent window and the detector array such that back-emitted light collected by the micro optical element array is detected by the detector array to form a scanned confocal image (e.g., to construct an optical slice of the sample), wherein: the position of the transparent window relative to the detector array is fixed (e.g., during imaging of the sample by the system), and the scanning stage and micro optical element array are confined (e.g., fully confined) within the system such that the scanning stage and micro optical element array are protected from the sample (e.g., and the outside environment) by the transparent window; an aperture stop for spatially filtering the back-emitted light (e.g., fluorescent light between 510-520 nm, or light with a wavelength greater than or equal to 490 nm and, in some implementations, less than 530 nm; between 491 nm and 520 nm), thereby rejecting out-of-focus light (e.g., filtering out collected sample information that does not originate from the foci of the micro optical elements prior to detection by the detector array), wherein the detector array comprises a plurality of detectors, each detector independently detecting a portion of the back-emitted light originating from a micro optical element in the micro optical element array; and a computing device comprising a processor and a memory storing instructions thereon that, when executed by the processor, cause the processor to construct an image representing an optical slice of the fresh tissue sample based on the back-emitted light detected by the detector array. 
         [0017]    In another aspect, the invention is directed to a system for in-operating-theatre imaging of fresh tissue samples resected during surgery (e.g., cancer surgery) for pathology assessment, the system comprising: a light source for providing (e.g., laser) an illumination beam that illuminates a fluorescent stained, fresh sample (e.g., a preserved sample—i.e., unsliced thereby preserving the sample for definitive assessment) held by a sample holder in an operating theatre; a beam expander (e.g., collimating lens) for expanding a waist of the illumination beam, thereby providing a collimated illumination beam; a beam splitter (e.g., dichroic mirror/filter, prism, or grating(s)), located between the sample and a detector array, for directing the collimated illumination beam toward a micro optical element array (e.g., using refractive lenses, Fresnel zone plates, micro reflective objectives, and/or GRIN lenses; e.g., a micro lens array); the micro optical element array for focusing the collimated illumination beam from the beam splitter onto the sample, thereby forming an array of tight foci for exciting the fluorescence in the sample to produce back-emitted light, wherein: the micro optical element array collects back-emitted light from the sample, and the collected back-emitted light propagates (e.g., as individual collimated beams) and is directed (e.g., by a set of optics) to a detector array; and a gap (e.g., an airgap) of less than 500 μm (e.g., 50-150 μm, 80-120 μm) is maintained between the micro optical element array and a transparent window (e.g., glass, quartz, sapphire, plastic) onto which (e.g., above which) the sample is placed for imaging; a scanning stage for moving a position of the transparent window relative to the micro optical element array and the detector array such that back-emitted light collected by the micro optical element array is detected by the detector array to form a scanned confocal image (e.g., to construct an optical slice of the sample), wherein the position of the micro optical element array relative to the detector array is fixed (e.g., during imaging of the sample by the system); an aperture stop for spatially filtering the back-emitted light (e.g., fluorescent light between 510-520 nm, or light with a wavelength greater than or equal to 490 nm and, in some implementations, less than 530 nm, or between 491 nm and 520 nm), thereby rejecting out-of-focus light (e.g., filtering out collected sample information that is not originating from the foci of the micro optical elements prior to detection by the detector array), wherein the detector array comprises a plurality of detectors, each detector independently detecting a portion of the back-emitted light originating from a micro optical element in the micro optical element array; and a computing device comprising a processor and a memory storing instructions thereon that, when executed by the processor, cause the processor to construct an image representing an optical slice of the fresh tissue sample based on the back-emitted light detected by the detector array. 
         [0018]    In certain embodiments, the memory stores instructions thereon that, when executed by the processor, cause the processor to send, via a network, the image to a second computing device such that a pathologist in a remote location (e.g., outside of the operating theatre) can perform the pathology assessment. 
         [0019]    In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the sample. In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the collimated illumination beam. 
         [0020]    In certain embodiments, the system comprises a kinematic support structure having at least three feet of adjustable height, the support structure supporting the scanning stage such that the height and tilt of the transparent window relative to the micro optical element array and the corresponding optical path are adjustable. 
         [0021]    In certain embodiments, the system comprises a first flat mirror for reflecting the collimated illumination beam onto the beam splitter. In certain embodiments, the system comprises a second flat mirror for reflecting the collimated illumination beam from the beam splitter to the micro optical element array. In certain embodiments, the second flat mirror reflects the back-emitted light passed through the micro optical element array from the sample through the beam splitter. 
         [0022]    In certain embodiments, the system comprises a field lens for focusing the back-emitted light prior to spatially filtering the back-emitted light. 
         [0023]    In certain embodiments, the beam expander is a collimating lens. 
         [0024]    In certain embodiments, the ratio of detectors to micro optical elements is from 1:1 to 1:12 (e.g., about 1:1, 1:2, 1:3, 1:4, 1:6, 1:8, or 1:12, e.g., to the nearest whole number, or within a range of any two of these values). 
         [0025]    In certain embodiments, the micro optical element array comprises from 1000 to 100,000 micro optical elements (e.g., 1600 micro optical elements for a 10 mm field of view; 6400 micro optical elements for a 20 mm field of view, etc.). 
         [0026]    In certain embodiments, the sample is stained with a fluorescent stain (e.g., proflavine, acridine orange, hematoxylin or eosin). 
         [0027]    In certain embodiments, the system is configured for in-operating-theatre imaging of tissue (e.g., fresh) resected during surgery (e.g., cancer surgery) in less than 10 minutes (e.g., less than 5 minutes). 
         [0028]    In certain embodiments, the system comprises a first computing device for sending information regarding the detected back-emitted light (e.g., an image captured by the camera) to a second computing device (e.g., remote from the first computer device—i.e., outside the operating theatre). 
         [0029]    In certain embodiments, the sample holder is screwed onto the scanning stage. 
         [0030]    In certain embodiments, the scanning stage is a three axis positioning stage (e.g., a high precision positioning stage, e.g., with precision equal or better than one micrometer; in other embodiments, the stage is a two-axis positioning stage, e.g., high precision positioning stage). 
         [0031]    In certain embodiments, the sample holder comprises the transparent window. 
         [0032]    In certain embodiments, the transparent window is a thin transparent window (e.g., 25-50 μm, or 50-100 μm thick; e.g., thin glass with a thickness from 25-50 μm or 50-100 μm). 
         [0033]    In certain embodiments, the sample holder comprises a seal at the bottom of the transparent window to protect the system from sample liquid. 
         [0034]    In certain embodiments, the transparent window provides an optical interface (e.g., transparent and flat between the sample and the micro optical element array. 
         [0035]    In certain embodiments, the scanning stage is configured to bring the transparent window in close proximity to the micro optical element array (e.g., within 100 μm). 
         [0036]    In certain embodiments, the sample holder comprises a metallic body. 
         [0037]    In certain embodiments, the sample holder comprises an opening window (e.g., 40×20 mm, 10-50 mm by 10-50 mm; e.g., covered/filled by the transparent window). 
         [0038]    In certain embodiments, the scanning stage comprises a translation mechanism which is configured for establishing a relative motion between said sample and said micro optical element array. 
         [0039]    In certain embodiments, the sample is located in the focus area of the micro optical element array; and each micro optical element is configured to collect and direct sample information from the sample toward the detector. 
         [0040]    In certain embodiments, the sample holder is configured (e.g. is sized and shaped) to accommodate a sample having a thickness that is within a range of 0.5-20 mm (e.g., that is within a range of 3-5 mm, 5-10 mm, 7-15 mm, 10-25 mm, 15-30 mm, or 25-35 mm, and/or that is no less than 0.5 mm, no less than 1 mm, no less than 3 mm, or no less than 5 mm). 
         [0041]    In another aspect, the invention is directed to a method for in-operating-theatre imaging of fresh tissue samples resected during surgery (e.g., cancer surgery) for pathology assessment, the method comprising: providing, by a light source (e.g., laser or other light source providing light with a wavelength of 488 nm or between 450-490 nm), an illumination beam for illuminating a fluorescent stained, fresh sample (e.g., a fluorescent-stained fresh sample) (e.g., an unsliced sample preserved for definitive assessment in follow-up testing) held by a sample holder located in an operating theatre; directing a collimated light beam via illumination optics onto the fresh sample (e.g., the fresh fluorescent stained sample) held by the sample holder in the operating theatre, wherein the illumination optics comprise: a beam expander expanding a waist of the illumination beam, thereby providing the collimated illumination beam, a beam splitter (e.g., dichroic mirror/filter, prism, or grating(s)), located between the sample and a detector array, directing the collimated illumination beam toward a micro optical element array (e.g., the micro optical element array comprising refractive lenses, Fresnel zone plates, micro reflective objectives, and/or GRIN lenses; e.g., a micro lens array), and the micro optical element array for focusing the collimated illumination beam from the beam splitter onto the sample, thereby forming an array of tight foci for exciting the fluorescence in the sample to produce the back-emitted light, wherein: each micro optical element focuses a portion of the collimated illumination beam onto the sample, and a gap (e.g., airgap) of less than 500 μm (e.g., 50-150 μm, 80-120 μm) is maintained between the micro optical element array and a transparent window (e.g., glass, quartz, sapphire, plastic) onto which (e.g., above which) the sample is placed for imaging; directing the back-emitted light from the sample to the detector array via detecting optics, the detecting optics comprising: the micro optical element array, which collects the back-emitted light from the sample, which propagates (e.g., as individual collimated beams) and is directed (e.g., by a set of optics) to the detector array, and an aperture stop spatially filtering the back-emitted light, thereby rejecting out-of-focus light; moving, by a scanning stage, a position of the micro optical element array relative to the transparent window and the detector array such that back-emitted light focused by the micro optical element array is detected by the detector array to form a scanned confocal image (e.g., to construct an optical slice of the sample), wherein: the position of the transparent window relative to the detector array is fixed (e.g., during imaging of the sample by the system), and the scanning stage and micro optical element array are confined (e.g., fully confined) within the system such that the scanning stage and micro optical element array are protected from the sample (e.g., and the outside environment) by the transparent window; detecting, by the detector array, the back-emitted light filtered by the aperture stop, wherein the detector array comprises a plurality of detectors, each detector independently detecting a portion of the back-emitted light originating from a micro optical element in the micro optical element array; and constructing, by a processor of a computing device, an image representing an optical slice of the fresh tissue sample based on the back-emitted light detected by the detector array. 
         [0042]    In another aspect, the invention is directed to a method for in-operating-theatre imaging of fresh tissue resected during surgery (e.g., cancer surgery) for pathology assessment, the method comprising: providing, by a light source (e.g., laser or other light source providing light with a wavelength of 488 nm or between 450-490 nm), an illumination beam for illuminating a fluorescent stained, fresh sample (e.g., a preserved sample—i.e., unsliced thereby preserving the sample for definitive assessment) held by a sample holder in an operating theatre; directing a collimated light beam via illumination optics onto a fresh (e.g., fluorescent-stained) sample held by a sample holder in an operating theatre, wherein the illumination optics comprise: a beam expander expanding a waist of the illumination beam, thereby providing the collimated illumination beam, a beam splitter (e.g., dichroic mirror/filter, prism, or grating(s)), located between the sample and a detector array, directing the collimated illumination beam toward a micro optical element array (e.g., the micro optical element array comprising refractive lenses, Fresnel zone plates, micro reflective objectives, and/or GRIN lenses; e.g., a micro lens array), and the micro optical element array focusing the collimated illumination beam from the beam splitter onto the sample, thereby forming an array of tight foci for exciting the fluorescence in the sample to produce the back-emitted light, wherein: each micro optical element in the micro optical element array focuses a portion of the collimated illumination beam onto the sample, and a gap (e.g., airgap) of less than 500 μm (e.g., 50-150 μm, 80-120 μm) is maintained between the micro optical element array and a transparent window (e.g., glass, quartz, sapphire, plastic) onto which (e.g., above which) the sample is placed for imaging; directing the back-emitted light from the sample to the detector array via detecting optics, the detecting optics comprising: the micro optical element array, which collects the back-emitted light that propagates (e.g., as individual collimated beams) and is directed (e.g., by a set of optics) to a detector array, and an aperture stop spatially filtering the back-emitted light, thereby rejecting out-of-focus light; moving, by a scanning stage, a position of the transparent window relative to the micro optical element array and the detector array such that back-emitted light focused by the micro optical element array is detected by the detector array to form a scanned confocal image (e.g., to construct an optical slice of the sample, wherein the position of the micro optical element array relative to the detector array is fixed (e.g., during imaging of the sample by the system); detecting, by the detector array, the back-emitted light filtered by the aperture stop, wherein the detector array comprises a plurality of detectors, each detector independently detecting a portion of the back-emitted light originating from a micro optical element in the micro optical element array; and constructing, by a processor of a computing device, an image representing an optical slice of the fresh tissue sample based on the back-emitted light detected by the detector array. 
         [0043]    In certain embodiments, the method comprises sending, by the processor, via a network, the image to a second computing device such that a pathologist in a remote location (e.g., outside of the operating theatre) can perform the pathology assessment. 
         [0044]    In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the sample. 
         [0045]    In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the collimated illumination beam. 
         [0046]    In certain embodiments, a kinematic support structure having at least three feet of adjustable height supports the scanning stage such that the height and tilt of the transparent window relative to the micro optical element array (e.g., and the corresponding optical path) are adjustable. 
         [0047]    In certain embodiments, the illumination optics comprises: a first flat mirror reflecting the collimated illumination beam onto the beam splitter. In certain embodiments, the illumination optics comprises: a second flat mirror reflecting the collimated illumination beam from the beam splitter to the micro optical element array. In certain embodiments, the second flat mirror reflects the back-emitted light passed through the micro optical element array from the sample through the beam splitter. 
         [0048]    In certain embodiments, the detection optics comprises: a field lens focusing the back-emitted light prior to spatially filtering the back-emitted light. 
         [0049]    In certain embodiments, the beam expander is a collimating lens. 
         [0050]    In certain embodiments, the ratio of detectors to micro optical elements is from 1:1 to 1:12 (e.g., about 1:1, 1:2, 1:3, 1:4, 1:6, 1:8, or 1:12, e.g., to the nearest whole number, or within a range of any two of these values). 
         [0051]    In certain embodiments, the micro optical element array comprises from 1000 to 100,000 micro optical elements (e.g., 1600 micro optical elements for a 10 mm field of view; 6400 micro optical elements for a 20 mm field of view, etc.). 
         [0052]    In certain embodiments, the sample is stained with a fluorescent stain (e.g., proflavine, acridine orange, hematoxylin or eosin). 
         [0053]    In certain embodiments, the method is performed in less than 10 minutes (e.g., less than 5 minutes). 
         [0054]    In certain embodiments, the method comprises sending, by a processor of a first computing device, to a second computing device (e.g., remote from the first computer device—i.e., outside the operating theatre) information regarding the detected back-emitted light (e.g., an image captured by the camera). 
         [0055]    In certain embodiments, the method comprises, prior to providing an illumination beam for illuminating the sample: staining the sample with a fluorescent stain; and placing the sample in/on the sampler holder. 
         [0056]    In certain embodiments, the sample holder is screwed onto the scanning stage. 
         [0057]    In certain embodiments, the scanning stage is a three axis positioning stage (e.g., high precision positioning stage; e.g., in other embodiments, the scanning stage is a two-axis positioning stage, e.g., high precision positioning stage). 
         [0058]    In certain embodiments, the sample holder comprises the transparent window. 
         [0059]    In certain embodiments, the transparent window is a thin transparent window (e.g., 25-50 μm, or 50-100 μm thick). 
         [0060]    In certain embodiments, the sample holder comprises a seal at the bottom of the transparent window to protect the system from sample liquid. 
         [0061]    In certain embodiments, the transparent window provides an optical interface (e.g., transparent and flat) between the sample and the micro optical element array. 
         [0062]    In certain embodiments, the scanning stage brings the transparent window in close proximity to the micro optical element array (e.g., within 100 μm). 
         [0063]    In certain embodiments, the sample holder comprises a metallic body. 
         [0064]    In certain embodiments, the sample holder comprises an opening (e.g., 40×20 mm, 10-50 mm by 10-50 mm) covered/filled by the transparent window. 
         [0065]    In certain embodiments, the scanning stage comprises a translation system for establishing a relative motion between the sample and the micro optical element array. 
         [0066]    In certain embodiments, the sample is located in the focus area of the micro optical element array; and each micro optical element is configured to collect and direct sample information from the sample towards the detector. 
         [0067]    In certain embodiments, the sample has a thickness that is within a range of 0.5-20 mm (e.g., that is within a range of 3-5 mm, 5-10 mm, 7-15 mm, 10-25 mm, 15-30 mm, or 25-35 mm, and/or that is no less than 0.5 mm, no less than 1 mm, no less than 3 mm, or no less than 5 mm). 
         [0068]    In another aspect, the invention is directed to a method for in-operating-theatre imaging of tissue (e.g., fresh tissue) resected during surgery (e.g., cancer surgery) for pathology assessment, the method comprising: intraoperatively resecting tissue to obtain a fresh tissue sample; procuring an image of the fresh tissue sample (e.g., using an embodiment of the system described herein); and sending, by a processor of a first computing device, to a second computing device (e.g., remote from the first computer device—i.e., outside the operating theatre) the image of the fresh tissue sample. 
         [0069]    In various embodiments, elements or features described with respect to one aspect of the invention can be used with respect to another aspect of the invention (e.g., any limitation described with respect to a system embodiment of the invention can apply to a method embodiment of the invention, and vice versa). 
         [0070]    In another aspect, the disclosed technology includes a system for in-operating-theatre imaging of fresh tissue samples resected during surgery (e.g., cancer surgery) for pathology assessment, the system including: a light source for providing (e.g., laser or other light source providing light with a wavelength of 488 nm or between 450-490 nm) an illumination beam that illuminates a fluorescent stained, fresh sample (e.g., a fluorescent-stained fresh sample) (e.g., an unsliced sample preserved for definitive assessment in follow-up testing), wherein the fresh sample is held by a sample holder located in an operating theatre; a beam expander (e.g., collimating lens (e.g., for use with a monomode fibered laser) or a telecentric afocal magnification relay (e.g., for use with a collimated laser)) for expanding the waist of the illumination beam to a size comparable to the field of view to be illuminated, thereby providing a collimated illumination beam; a beam splitter (e.g., dichroic mirror/filter, prism, or grating(s)) located between the sample and a detector array, for directing the collimated illumination beam toward a micro optical element array; the micro optical element array (e.g., comprising refractive lenses, Fresnel zone plates, micro reflective objectives, and/or GRIN lenses; e.g., a micro lens array) for focusing the collimated illumination beam from the beam splitter onto the sample, thereby forming an array of tight foci for exciting the fluorescence in the sample to produce the back-emitted light, wherein the micro optical element array is configured such that: the micro optical element array collects back-emitted light from the sample, and the collected back-emitted light propagates (e.g., as individual collimated beams) and is directed (e.g., by a set of optics) to a detector array; and a gap (e.g., an airgap) of less than 500 μm (e.g., 50-150 μm, 80-120 μm) is maintained between the micro optical element array and a window (e.g., a transparent window, e.g., made of glass, quartz, sapphire, plastic) onto which (e.g., above which) the sample is placed for imaging; a scanning stage for moving a position of the micro optical element array relative to the transparent window and the detector array such that back-emitted light collected by the micro optical element array is detected by the detector array to form a scanned confocal image (e.g., to construct an optical slice of the sample), wherein: the position of the transparent window relative to the detector array is fixed (e.g., during imaging of the sample by the system), and the scanning stage and micro optical element array are confined (e.g., fully confined) within the system such that the scanning stage and micro optical element array are protected from the sample (e.g., and the outside environment) by the transparent window; an aperture stop for spatially filtering the back-emitted light (e.g., fluorescent light between 510-520 nm, or light with a wavelength greater than or equal to 490 nm and, in some implementations, less than 530 nm; between 491 nm and 520 nm), thereby rejecting out-of-focus light (e.g., filtering out collected sample information that does not originate from the foci of the micro optical elements prior to detection by the detector array), wherein the detector array comprises a plurality of detectors, each detector independently detecting a portion of the back-emitted light originating from a micro optical element in the micro optical element array; and a computing device comprising a processor and a memory storing instructions thereon that, when executed by the processor, cause the processor to construct an image representing an optical slice of the fresh tissue sample based on the back-emitted light detected by the detector array. 
         [0071]    In certain embodiments, the memory stores instructions thereon that, when executed by the processor, cause the processor to send, via a network, the image to a second computing device such that a pathologist in a remote location (e.g., outside of the operating theatre) can perform the pathology assessment. 
         [0072]    In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the sample. 
         [0073]    In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the collimated illumination beam. 
         [0074]    In certain embodiments, the curved surface of each micro optical element has a conical shaped surface. 
         [0075]    In certain embodiments, the curved surface of each micro optical element has a hyperbolic shaped surface. 
         [0076]    In certain embodiments, the curved surface of each micro optical element has a conic constant from −1.8 to −2.2 (e.g., −2). 
         [0077]    In certain embodiments, each micro optical element has a Strehl ratio greater than or equal to 0.8. 
         [0078]    In certain embodiments, each micro optical element has a spot size from 0.2 μm to 5 μm, 0.2 μm to 1 μm, 0.3 μm to 0.6 μm, and 0.4 μm to 0.5 μm. 
         [0079]    In certain embodiments, a free working distance (i.e., a distance from the tip of the micro optical elements to a focal plane of the micro optical element array) is from 80 μm to 450 μm, 150 μm to 350 μm, or 250 μm to 300 μm. 
         [0080]    In certain embodiments, the micro optical element array has a focal plane from 10 μm to 200 μm, 20 μm to 150 μm, or 50 μm to 100 μm above the transparent window. 
         [0081]    In certain embodiments, the system includes a kinematic support structure having at least three feet (e.g., four) of adjustable height, the support structure supporting the scanning stage such that the height and tilt of the transparent window relative to the micro optical element array and the corresponding optical path are adjustable. 
         [0082]    In certain embodiments, the system includes a first flat mirror for reflecting the collimated illumination beam onto the beam splitter. 
         [0083]    In certain embodiments, the system includes a second flat mirror for reflecting the collimated illumination beam from the beam splitter to the micro optical element array. 
         [0084]    In certain embodiments, the second flat mirror reflects the back-emitted light passed through the micro optical element array from the sample through the beam splitter. 
         [0085]    In certain embodiments, the system includes a field lens for focusing the back-emitted light prior to spatially filtering the back-emitted light. 
         [0086]    In certain embodiments, the beam expander is a collimating lens. 
         [0087]    In certain embodiments, the ratio of micro optical elements to detectors is from 1:1 to 1:100, 1:5 to 1:80, 1:20 to 1:70, 1:30 to 1:60, or 1:40 to 1:50 (e.g., about 1:1, 1:2, 1:3, 1:4, 1:6, 1:8, or 1:12, e.g., to the nearest whole number, or within a range of any two of these values). 
         [0088]    In certain embodiments, the micro optical element array comprises from 1000 to 100,000 micro optical elements (e.g., 1600 micro optical elements for a 10 mm field of view; 6400 micro optical elements for a 20 mm field of view, etc.). 
         [0089]    In certain embodiments, the sample is stained with a fluorescent stain (e.g., proflavine, acridine orange, hematoxylin or eosin). 
         [0090]    In certain embodiments, the system is configured for in-operating-theatre imaging of tissue (e.g., fresh) resected during surgery (e.g., cancer surgery) in less than 10 minutes (e.g., less than 5 minutes). 
         [0091]    In certain embodiments, the system includes a first computing device for sending information regarding the detected back-emitted light (e.g., an image captured by the camera) to a second computing device (e.g., remote from the first computer device—i.e., outside the operating theatre). 
         [0092]    In certain embodiments, the system includes the sample holder is screwed onto the scanning stage. 
         [0093]    In certain embodiments, the scanning stage is a three axis positioning stage (e.g., a high precision positioning stage, e.g., with precision equal or better than one micrometer; in other embodiments, the stage is a two-axis positioning stage, e.g., high precision positioning stage). 
         [0094]    In certain embodiments, the sample holder comprises the transparent window. 
         [0095]    In certain embodiments, the transparent window is a thin transparent window (e.g., 50-100 μm, or 100-500 μm thick; e.g., thin glass with a thickness from 50-100 μm or 100-500 μm). 
         [0096]    In certain embodiments, the system includes an optical interface clamp (e.g., ring-shaped) that maintains the transparent window in place. 
         [0097]    In certain embodiments, the sample holder comprises a seal at the bottom of the transparent window to protect the system from sample liquid. 
         [0098]    In certain embodiments, the transparent window provides an optical interface (e.g., transparent and flat between the sample and the micro optical element array. 
         [0099]    In certain embodiments, the scanning stage is configured to bring the transparent window in close proximity to the micro optical element array (e.g., within 100 μm). 
         [0100]    In certain embodiments, the sample holder comprises a metallic body. 
         [0101]    In certain embodiments, the sample holder comprises an opening window (e.g., 40×20 mm, 10-50 mm by 10-50 mm; e.g., covered/filled by the transparent window). 
         [0102]    In certain embodiments, the scanning stage comprises a translation mechanism which is configured for establishing a relative motion between said sample and said micro optical element array. 
         [0103]    In certain embodiments, the sample is located in the focus area of the micro optical element array; and each micro optical element is configured to collect and direct sample information from the sample toward the detector. 
         [0104]    In certain embodiments, the sample holder is configured (e.g. is sized and shaped) to accommodate a sample having a thickness that is within a range of 0.5-20 mm (e.g., that is within a range of 3-5 mm, 5-10 mm, 7-15 mm, 10-25 mm, 15-30 mm, or 25-35 mm, and/or that is no less than 0.5 mm, no less than 1 mm, no less than 3 mm, or no less than 5 mm). 
         [0105]    In certain embodiments, the system includes a mobile cart. 
         [0106]    In certain embodiments, the system includes an attachment system for attaching a removable sample holder to the scanning stage. 
         [0107]    In certain embodiments, the attachment system comprises a support base mounted on the scanning stage, the support base having a mount with one or more protrusions extending from the mount, wherein the mount is hollow on the inside and the support base has a corresponding opening therein such that an optical chip can scan a sample through the support base. 
         [0108]    In another aspect, the disclosed technology includes a system for in-operating-theatre imaging of fresh tissue samples resected during surgery (e.g., cancer surgery) for pathology assessment, the system including: a light source for providing (e.g., laser) an illumination beam that illuminates a fluorescent stained, fresh sample (e.g., a preserved sample—i.e., unsliced thereby preserving the sample for definitive assessment) held by a sample holder in an operating theatre; a beam expander (e.g., collimating lens) for expanding a waist of the illumination beam, thereby providing a collimated illumination beam; a beam splitter (e.g., dichroic mirror/filter, prism, or grating(s)), located between the sample and a detector array, for directing the collimated illumination beam toward a micro optical element array (e.g., using refractive lenses, Fresnel zone plates, micro reflective objectives, and/or GRIN lenses; e.g., a micro lens array); the micro optical element array for focusing the collimated illumination beam from the beam splitter onto the sample, thereby forming an array of tight foci for exciting the fluorescence in the sample to produce back-emitted light, wherein: the micro optical element array collects back-emitted light from the sample, and the collected back-emitted light propagates (e.g., as individual collimated beams) and is directed (e.g., by a set of optics) to a detector array; and a gap (e.g., an airgap) of less than 500 μm (e.g., 50-150 μm, 80-120 μm) is maintained between the micro optical element array and a transparent window (e.g., glass, quartz, sapphire, plastic) onto which (e.g., above which) the sample is placed for imaging; a scanning stage for moving a position of the transparent window relative to the micro optical element array and the detector array such that back-emitted light collected by the micro optical element array is detected by the detector array to form a scanned confocal image (e.g., to construct an optical slice of the sample), wherein the position of the micro optical element array relative to the detector array is fixed (e.g., during imaging of the sample by the system); an aperture stop for spatially filtering the back-emitted light (e.g., fluorescent light between 510-520 nm, or light with a wavelength greater than or equal to 490 nm and, in some implementations, less than 530 nm, or between 491 nm and 520 nm), thereby rejecting out-of-focus light (e.g., filtering out collected sample information that is not originating from the foci of the micro optical elements prior to detection by the detector array), wherein the detector array comprises a plurality of detectors, each detector independently detecting a portion of the back-emitted light originating from a micro optical element in the micro optical element array; and a computing device comprising a processor and a memory storing instructions thereon that, when executed by the processor, cause the processor to construct an image representing an optical slice of the fresh tissue sample based on the back-emitted light detected by the detector array. 
         [0109]    In certain embodiments, the memory stores instructions thereon that, when executed by the processor, cause the processor to send, via a network, the image to a second computing device such that a pathologist in a remote location (e.g., outside of the operating theatre) can perform the pathology assessment. 
         [0110]    In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the sample. 
         [0111]    In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the collimated illumination beam. 
         [0112]    In certain embodiments, the curved surface of each micro optical element has a conical shaped surface. 
         [0113]    In certain embodiments, the curved surface of each micro optical element has a hyperbolic shaped surface. 
         [0114]    In certain embodiments, the curved surface of each micro optical element has a conic constant from −1.8 to −2.2 (e.g., −2). 
         [0115]    In certain embodiments, each micro optical element has a Strehl ratio greater than or equal to 0.8. 
         [0116]    In certain embodiments, each micro optical element has a spot size from 0.2 μm to 5 μm, 0.2 μm to 1 μm, 0.3 μm to 0.6 μm, and 0.4 μm to 0.5 μm. 
         [0117]    In certain embodiments, a free working distance (i.e., a distance from the tip of the micro optical elements to a focal plane of the micro optical element array) is from 80 μm to 450 μm, 150 μm to 350 μm, or 250 μm to 300 μm. 
         [0118]    In certain embodiments, the micro optical element array has a focal plane from 10 μm to 200 μm, 20 μm to 150 μm, or 50 μm to 100 μm above the transparent window. 
         [0119]    In certain embodiments, the system includes a kinematic support structure having at least three feet (e.g., four) of adjustable height, the support structure supporting the scanning stage such that the height and tilt of the transparent window relative to the micro optical element array and the corresponding optical path are adjustable. 
         [0120]    In certain embodiments, the system includes a first flat mirror for reflecting the collimated illumination beam onto the beam splitter. 
         [0121]    In certain embodiments, the system includes a second flat mirror for reflecting the collimated illumination beam from the beam splitter to the micro optical element array. 
         [0122]    In certain embodiments, the second flat mirror reflects the back-emitted light passed through the micro optical element array from the sample through the beam splitter. 
         [0123]    In certain embodiments, the system includes a field lens for focusing the back-emitted light prior to spatially filtering the back-emitted light. 
         [0124]    In certain embodiments, the beam expander is a collimating lens. 
         [0125]    In certain embodiments, the ratio of micro optical elements to detectors is from 1:1 to 1:100, 1:5 to 1:80, 1:20 to 1:70, 1:30 to 1:60, or 1:40 to 1:50 (e.g., about 1:1, 1:2, 1:3, 1:4, 1:6, 1:8, or 1:12, e.g., to the nearest whole number, or within a range of any two of these values). 
         [0126]    In certain embodiments, the micro optical element array comprises from 1000 to 100,000 micro optical elements (e.g., 1600 micro optical elements for a 10 mm field of view; 6400 micro optical elements for a 20 mm field of view, etc.). 
         [0127]    In certain embodiments, the sample is stained with a fluorescent stain (e.g., proflavine, acridine orange, hematoxylin or eosin). 
         [0128]    In certain embodiments, the system is configured for in-operating-theatre imaging of tissue (e.g., fresh) resected during surgery (e.g., cancer surgery) in less than 10 minutes (e.g., less than 5 minutes). 
         [0129]    In certain embodiments, the system includes a first computing device for sending information regarding the detected back-emitted light (e.g., an image captured by the camera) to a second computing device (e.g., remote from the first computer device—i.e., outside the operating theatre). 
         [0130]    In certain embodiments, the system includes the sample holder is screwed onto the scanning stage. 
         [0131]    In certain embodiments, the scanning stage is a three axis positioning stage (e.g., a high precision positioning stage, e.g., with precision equal or better than one micrometer; in other embodiments, the stage is a two-axis positioning stage, e.g., high precision positioning stage). 
         [0132]    In certain embodiments, the sample holder comprises the transparent window. 
         [0133]    In certain embodiments, the transparent window is a thin transparent window (e.g., 50-100 μm, or 100-500 μm thick; e.g., thin glass with a thickness from 50-100 μm or 100-500 μm). 
         [0134]    In certain embodiments, the system includes an optical interface clamp (e.g., ring-shaped) that maintains the transparent window in place. 
         [0135]    In certain embodiments, the sample holder comprises a seal at the bottom of the transparent window to protect the system from sample liquid. 
         [0136]    In certain embodiments, the transparent window provides an optical interface (e.g., transparent and flat between the sample and the micro optical element array. 
         [0137]    In certain embodiments, the scanning stage is configured to bring the transparent window in close proximity to the micro optical element array (e.g., within 100 μm). 
         [0138]    In certain embodiments, the sample holder comprises a metallic body. 
         [0139]    In certain embodiments, the sample holder comprises an opening window (e.g., 40×20 mm, 10-50 mm by 10-50 mm; e.g., covered/filled by the transparent window). 
         [0140]    In certain embodiments, the scanning stage comprises a translation mechanism which is configured for establishing a relative motion between said sample and said micro optical element array. 
         [0141]    In certain embodiments, the sample is located in the focus area of the micro optical element array; and each micro optical element is configured to collect and direct sample information from the sample toward the detector. 
         [0142]    In certain embodiments, the sample holder is configured (e.g. is sized and shaped) to accommodate a sample having a thickness that is within a range of 0.5-20 mm (e.g., that is within a range of 3-5 mm, 5-10 mm, 7-15 mm, 10-25 mm, 15-30 mm, or 25-35 mm, and/or that is no less than 0.5 mm, no less than 1 mm, no less than 3 mm, or no less than 5 mm). 
         [0143]    In certain embodiments, the system includes a mobile cart. 
         [0144]    In certain embodiments, the system includes an attachment system for attaching a removable sample holder to the scanning stage. 
         [0145]    In certain embodiments, the attachment system comprises a support base mounted on the scanning stage, the support base having a mount with one or more protrusions extending from the mount, wherein the mount is hollow on the inside and the support base has a corresponding opening therein such that an optical chip can scan a sample through the support base. 
         [0146]    In another aspect, the disclosed technology includes a method for in-operating-theatre imaging of fresh tissue samples resected during surgery (e.g., cancer surgery) for pathology assessment, the method including: providing, by a light source (e.g., laser or other light source providing light with a wavelength of 488 nm or between 450-490 nm), an illumination beam for illuminating a fluorescent stained, fresh sample (e.g., a fluorescent-stained fresh sample) (e.g., an unsliced sample preserved for definitive assessment in follow-up testing) held by a sample holder located in an operating theatre; directing a collimated light beam via illumination optics onto the fresh sample (e.g., the fresh fluorescent stained sample) held by the sample holder in the operating theatre, wherein the illumination optics comprise: a beam expander expanding a waist of the illumination beam, thereby providing the collimated illumination beam, a beam splitter (e.g., dichroic mirror/filter, prism, or grating(s)), located between the sample and a detector array, directing the collimated illumination beam toward a micro optical element array (e.g., the micro optical element array comprising refractive lenses, Fresnel zone plates, micro reflective objectives, and/or GRIN lenses; e.g., a micro lens array), and the micro optical element array for focusing the collimated illumination beam from the beam splitter onto the sample, thereby forming an array of tight foci for exciting the fluorescence in the sample to produce the back-emitted light, wherein: each micro optical element focuses a portion of the collimated illumination beam onto the sample, and a gap (e.g., airgap) of less than 500 μm (e.g., 50-150 μm, 80-120 μm) is maintained between the micro optical element array and a transparent window (e.g., glass, quartz, sapphire, plastic) onto which (e.g., above which) the sample is placed for imaging; directing the back-emitted light from the sample to the detector array via detecting optics, the detecting optics comprising: the micro optical element array, which collects the back-emitted light from the sample, which propagates (e.g., as individual collimated beams) and is directed (e.g., by a set of optics) to the detector array, and an aperture stop spatially filtering the back-emitted light, thereby rejecting out-of-focus light; moving, by a scanning stage, a position of the micro optical element array relative to the transparent window and the detector array such that back-emitted light focused by the micro optical element array is detected by the detector array to form a scanned confocal image (e.g., to construct an optical slice of the sample), wherein: the position of the transparent window relative to the detector array is fixed (e.g., during imaging of the sample by the system), and the scanning stage and micro optical element array are confined (e.g., fully confined) within the system such that the scanning stage and micro optical element array are protected from the sample (e.g., and the outside environment) by the transparent window; detecting, by the detector array, the back-emitted light filtered by the aperture stop, wherein the detector array comprises a plurality of detectors, each detector independently detecting a portion of the back-emitted light originating from a micro optical element in the micro optical element array; and constructing, by a processor of a computing device, an image representing an optical slice of the fresh tissue sample based on the back-emitted light detected by the detector array. 
         [0147]    In certain embodiments, the method includes sending, by the processor, via a network, the image to a second computing device such that a pathologist in a remote location (e.g., outside of the operating theatre) can perform the pathology assessment. 
         [0148]    In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the sample. 
         [0149]    In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the collimated illumination beam. 
         [0150]    In certain embodiments, the curved surface of each micro optical element has a conical shaped surface. 
         [0151]    In certain embodiments, the curved surface of each micro optical element has a hyperbolic shaped surface. 
         [0152]    In certain embodiments, the curved surface of each micro optical element has a conic constant from −1.8 to −2.2 (e.g., −2). 
         [0153]    In certain embodiments, each micro optical element has a Strehl ratio greater than or equal to 0.8. 
         [0154]    In certain embodiments, each micro optical element has a spot size of 0.1 μm to 2 μm, 0.2 μm to 1 μm, 0.3 μm to 0.6 μm, or 0.4 μm to 0.5 μm. 
         [0155]    In certain embodiments, a free working distance (i.e., a distance from the tip of the micro optical elements to a focal plane of the micro optical element array) is from 80 μm to 450 μm, 150 μm to 350 μm, or 250 μm to 300 μm. 
         [0156]    In certain embodiments, the micro optical element array has a focal plane from 10 μm to 200 μm, 20 μm to 150 μm, or 50 μm to 100 μm above the transparent window. 
         [0157]    In certain embodiments, a kinematic support structure having at least three feet (e.g., four) of adjustable height supports the scanning stage such that the height and tilt of the transparent window relative to the micro optical element array (e.g., and the corresponding optical path) are adjustable. 
         [0158]    In certain embodiments, the illumination optics includes: a first flat mirror reflecting the collimated illumination beam onto the beam splitter. 
         [0159]    In certain embodiments, the illumination optics includes a second flat mirror reflecting the collimated illumination beam from the beam splitter to the micro optical element array. 
         [0160]    In certain embodiments, the second flat mirror reflects the back-emitted light passed through the micro optical element array from the sample through the beam splitter. 
         [0161]    In certain embodiments, the detection optics comprises: a field lens focusing the back-emitted light prior to spatially filtering the back-emitted light. 
         [0162]    In certain embodiments, the beam expander is a collimating lens. 
         [0163]    In certain embodiments, the ratio of detectors to micro optical elements is from 1:1 to 1:100, 1:5 to 1:80, 1:20 to 1:70, 1:30 to 1:60, or 1:40 to 1:50 (e.g., about 1:1, 1:2, 1:3, 1:4, 1:6, 1:8, or 1:12, e.g., to the nearest whole number, or within a range of any two of these values). 
         [0164]    In certain embodiments, the micro optical element array comprises from 1000 to 100,000 micro optical elements (e.g., 1600 micro optical elements for a 10 mm field of view; 6400 micro optical elements for a 20 mm field of view, etc.). 
         [0165]    In certain embodiments, the sample is stained with a fluorescent stain (e.g., proflavine, acridine orange, hematoxylin or eosin). 
         [0166]    In certain embodiments, the method is performed in less than 10 minutes (e.g., less than 5 minutes). 
         [0167]    In certain embodiments, the method includes sending, by a processor of a first computing device, to a second computing device (e.g., remote from the first computer device—i.e., outside the operating theatre) information regarding the detected back-emitted light (e.g., an image captured by the camera). 
         [0168]    In certain embodiments, the method includes, prior to providing an illumination beam for illuminating the sample: staining the sample with a fluorescent stain; and placing the sample in/on the sampler holder. 
         [0169]    In certain embodiments, the sample holder is screwed onto the scanning stage. 
         [0170]    In certain embodiments, the scanning stage is a three axis positioning stage (e.g., high precision positioning stage; e.g., in other embodiments, the scanning stage is a two-axis positioning stage, e.g., high precision positioning stage). 
         [0171]    In certain embodiments, the sample holder comprises the transparent window. 
         [0172]    In certain embodiments, the transparent window is a thin transparent window (e.g., 50-100 μm, or 100-500 μm thick; e.g., thin glass with a thickness from 50-100 μm or 100-500 μm). 
         [0173]    In certain embodiments, the sample holder comprises a seal at the bottom of the transparent window to protect the system from sample liquid. 
         [0174]    In certain embodiments, the transparent window provides an optical interface (e.g., transparent and flat) between the sample and the micro optical element array. 
         [0175]    In certain embodiments, the scanning stage brings the transparent window in close proximity to the micro optical element array (e.g., within 100 μm). 
         [0176]    In certain embodiments, the sample holder comprises a metallic body. 
         [0177]    In certain embodiments, the sample holder comprises an opening (e.g., 40×20 mm, 10-50 mm by 10-50 mm) covered/filled by the transparent window. 
         [0178]    In certain embodiments, the scanning stage comprises a translation system for establishing a relative motion between the sample and the micro optical element array. 
         [0179]    In certain embodiments, the sample is located in the focus area of the micro optical element array; and each micro optical element is configured to collect and direct sample information from the sample towards the detector. 
         [0180]    In certain embodiments, the sample has a thickness that is within a range of 0.5-20 mm (e.g., that is within a range of 3-5 mm, 5-10 mm, 7-15 mm, 10-25 mm, 15-30 mm, or 25-35 mm, and/or that is no less than 0.5 mm, no less than 1 mm, no less than 3 mm, or no less than 5 mm). 
         [0181]    In another aspect, the disclosed technology includes the disclosed technology includes a method for in-operating-theatre imaging of fresh tissue resected during surgery (e.g., cancer surgery) for pathology assessment, the method including: providing, by a light source (e.g., laser or other light source providing light with a wavelength of 488 nm or between 450-490 nm), an illumination beam for illuminating a fluorescent stained, fresh sample (e.g., a preserved sample—i.e., unsliced thereby preserving the sample for definitive assessment) held by a sample holder in an operating theatre; directing a collimated light beam via illumination optics onto a fresh (e.g., fluorescent-stained) sample held by a sample holder in an operating theatre, wherein the illumination optics comprise: a beam expander expanding a waist of the illumination beam, thereby providing the collimated illumination beam, a beam splitter (e.g., dichroic mirror/filter, prism, or grating(s)), located between the sample and a detector array, directing the collimated illumination beam toward a micro optical element array (e.g., the micro optical element array comprising refractive lenses, Fresnel zone plates, micro reflective objectives, and/or GRIN lenses; e.g., a micro lens array), and the micro optical element array focusing the collimated illumination beam from the beam splitter onto the sample, thereby forming an array of tight foci for exciting the fluorescence in the sample to produce the back-emitted light, wherein: each micro optical element in the micro optical element array focuses a portion of the collimated illumination beam onto the sample, and a gap (e.g., airgap) of less than 500 μm (e.g., 50-150 μm, 80-120 μm) is maintained between the micro optical element array and a transparent window (e.g., glass, quartz, sapphire, plastic) onto which (e.g., above which) the sample is placed for imaging; directing the back-emitted light from the sample to the detector array via detecting optics, the detecting optics comprising: the micro optical element array, which collects the back-emitted light that propagates (e.g., as individual collimated beams) and is directed (e.g., by a set of optics) to a detector array, and an aperture stop spatially filtering the back-emitted light, thereby rejecting out-of-focus light; moving, by a scanning stage, a position of the transparent window relative to the micro optical element array and the detector array such that back-emitted light focused by the micro optical element array is detected by the detector array to form a scanned confocal image (e.g., to construct an optical slice of the sample, wherein the position of the micro optical element array relative to the detector array is fixed (e.g., during imaging of the sample by the system); detecting, by the detector array, the back-emitted light filtered by the aperture stop, wherein the detector array comprises a plurality of detectors, each detector independently detecting a portion of the back-emitted light originating from a micro optical element in the micro optical element array; and constructing, by a processor of a computing device, an image representing an optical slice of the fresh tissue sample based on the back-emitted light detected by the detector array. 
         [0182]    In certain embodiments, the method includes sending, by the processor, via a network, the image to a second computing device such that a pathologist in a remote location (e.g., outside of the operating theatre) can perform the pathology assessment. 
         [0183]    In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the sample. 
         [0184]    In certain embodiments, the micro optical element array comprises a plurality of micro optical elements having curved surfaces facing the collimated illumination beam. 
         [0185]    In certain embodiments, the curved surface of each micro optical element has a conical shaped surface. 
         [0186]    In certain embodiments, the curved surface of each micro optical element has a hyperbolic shaped surface. 
         [0187]    In certain embodiments, the curved surface of each micro optical element has a conic constant from −1.8 to −2.2 (e.g., −2). 
         [0188]    In certain embodiments, each micro optical element has a Strehl ratio greater than or equal to 0.8. 
         [0189]    In certain embodiments, each micro optical element has a spot size of 0.1 μm to 2 μm, 0.2 μm to 1 μm, 0.3 μm to 0.6 μm, or 0.4 μm to 0.5 μm. 
         [0190]    In certain embodiments, a free working distance (i.e., a distance from the tip of the micro optical elements to a focal plane of the micro optical element array) is from 80 μm to 450 μm, 150 μm to 350 μm, or 250 μm to 300 μm. 
         [0191]    In certain embodiments, the micro optical element array has a focal plane from 10 μm to 200 μm, 20 μm to 150 μm, or 50 μm to 100 μm above the transparent window. 
         [0192]    In certain embodiments, a kinematic support structure having at least three feet (e.g., four) of adjustable height supports the scanning stage such that the height and tilt of the transparent window relative to the micro optical element array (e.g., and the corresponding optical path) are adjustable. 
         [0193]    In certain embodiments, the illumination optics includes: a first flat mirror reflecting the collimated illumination beam onto the beam splitter. 
         [0194]    In certain embodiments, the illumination optics includes a second flat mirror reflecting the collimated illumination beam from the beam splitter to the micro optical element array. 
         [0195]    In certain embodiments, the second flat mirror reflects the back-emitted light passed through the micro optical element array from the sample through the beam splitter. 
         [0196]    In certain embodiments, the detection optics comprises: a field lens focusing the back-emitted light prior to spatially filtering the back-emitted light. 
         [0197]    In certain embodiments, the beam expander is a collimating lens. 
         [0198]    In certain embodiments, the ratio of detectors to micro optical elements is from 1:1 to 1:100, 1:5 to 1:80, 1:20 to 1:70, 1:30 to 1:60, or 1:40 to 1:50 (e.g., about 1:1, 1:2, 1:3, 1:4, 1:6, 1:8, or 1:12, e.g., to the nearest whole number, or within a range of any two of these values). 
         [0199]    In certain embodiments, the micro optical element array comprises from 1000 to 100,000 micro optical elements (e.g., 1600 micro optical elements for a 10 mm field of view; 6400 micro optical elements for a 20 mm field of view, etc.). 
         [0200]    In certain embodiments, the sample is stained with a fluorescent stain (e.g., proflavine, acridine orange, hematoxylin or eosin). 
         [0201]    In certain embodiments, the method is performed in less than 10 minutes (e.g., less than 5 minutes). 
         [0202]    In certain embodiments, the method includes sending, by a processor of a first computing device, to a second computing device (e.g., remote from the first computer device—i.e., outside the operating theatre) information regarding the detected back-emitted light (e.g., an image captured by the camera). 
         [0203]    In certain embodiments, the method includes, prior to providing an illumination beam for illuminating the sample: staining the sample with a fluorescent stain; and placing the sample in/on the sampler holder. 
         [0204]    In certain embodiments, the sample holder is screwed onto the scanning stage. 
         [0205]    In certain embodiments, the scanning stage is a three axis positioning stage (e.g., high precision positioning stage; e.g., in other embodiments, the scanning stage is a two-axis positioning stage, e.g., high precision positioning stage). 
         [0206]    In certain embodiments, the sample holder comprises the transparent window. 
         [0207]    In certain embodiments, the transparent window is a thin transparent window (e.g., 50-100 μm, or 100-500 μm thick; e.g., thin glass with a thickness from 50-100 μm or 100-500 μm). 
         [0208]    In certain embodiments, the sample holder comprises a seal at the bottom of the transparent window to protect the system from sample liquid. 
         [0209]    In certain embodiments, the transparent window provides an optical interface (e.g., transparent and flat) between the sample and the micro optical element array. 
         [0210]    In certain embodiments, the scanning stage brings the transparent window in close proximity to the micro optical element array (e.g., within 100 μm). 
         [0211]    In certain embodiments, the sample holder comprises a metallic body. 
         [0212]    In certain embodiments, the sample holder comprises an opening (e.g., 40×20 mm, 10-50 mm by 10-50 mm) covered/filled by the transparent window. 
         [0213]    In certain embodiments, the scanning stage comprises a translation system for establishing a relative motion between the sample and the micro optical element array. 
         [0214]    In certain embodiments, the sample is located in the focus area of the micro optical element array; and each micro optical element is configured to collect and direct sample information from the sample towards the detector. 
         [0215]    In certain embodiments, the sample has a thickness that is within a range of 0.5-20 mm (e.g., that is within a range of 3-5 mm, 5-10 mm, 7-15 mm, 10-25 mm, 15-30 mm, or 25-35 mm, and/or that is no less than 0.5 mm, no less than 1 mm, no less than 3 mm, or no less than 5 mm). 
         [0216]    In another aspect, the disclosed technology includes a method for in-operating-theatre imaging of tissue (e.g., fresh tissue) resected during surgery (e.g., cancer surgery) for pathology assessment, the method including: intraoperatively resecting tissue to obtain a fresh tissue sample; procuring an image of the fresh tissue sample (e.g., using the system of any one of claims  1  to  39 ); and sending, by a processor of a first computing device, to a second computing device (e.g., remote from the first computer device—i.e., outside the operating theatre) the image of the fresh tissue sample. 
         [0217]    In another aspect, the disclosed technology includes a sample holding device, including: a support base that can be mounted on a pathology system, the support base comprising a mount having one or more protrusions extending from the mount, wherein the mount is hollow on the inside and the support base has a corresponding opening therein such that an optical chip can scan a sample through the support base; and a removable sample holder that is removably attachable to the support base, the removable sample holder comprising: a housing having an opening therethrough with one or more (e.g., two) interior protrusions extending into the opening, wherein the size and shape (e.g., round, cylindrical, circular) of the opening in the housing is such that the removable sample holder can be attached over the support base and twisted such that the one or more interior protrusions of the removable sample holder engage the one or more protrusions of the support base, thereby securing the removable sample holder to the support base; and a transparent window on which the sample can be placed and through which the optical chip can image the sample. 
     
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         [0218]    The foregoing and other objects, aspects, features, and advantages of the present disclosure will become more apparent and better understood by referring to the following description taken in conjunction with the accompanying drawings, in which: 
           [0219]      FIG. 1A  is a side view of an example system for in-operating-theatre of fresh thick tissue resected during surgery, in accordance with an embodiment of the invention; 
           [0220]      FIG. 1B  is a top view of an example system for in-operating-theatre of fresh thick tissue resected during surgery, in accordance with an embodiment of the invention; 
           [0221]      FIGS. 2A-C  are photographs of an example system for in-operating-theatre of fresh thick tissue resected during surgery, in accordance with an embodiment of the invention; 
           [0222]      FIG. 3  is a flowchart of an example method for imaging a sample, in accordance with an embodiment of the invention; 
           [0223]      FIGS. 4A-G  are illustrations of an example system for in-operating-theatre of fresh thick tissue resected during surgery, in accordance with an embodiment of the invention; 
           [0224]      FIG. 5  is an illustration of an example sample holder, in accordance with an embodiment of the invention; 
           [0225]      FIGS. 6A-6J  is an illustration of an example sample holder, in accordance with an embodiment of the invention; 
           [0226]      FIG. 7  is an illustration of an example structure for adjusting both height and tilt of the glass window (e.g., by moving the scanning stage) relative to the optical chip and corresponding optical path with an embodiment of the invention; 
           [0227]      FIG. 8  is an illustration of an example camera and pinhole assembly, in accordance with an embodiment of the invention; 
           [0228]      FIG. 9  is an illustration of an example optical chip scanning system, in accordance with an embodiment of the invention; 
           [0229]      FIGS. 10A-G  are illustrations of example systems for in-operating-theatre imaging of fresh thick tissue resected during surgery for pathology assessment, in accordance with embodiments of the invention; 
           [0230]      FIGS. 11A through 11C  illustrate an example implementation of a specimen imaging area, in accordance with an embodiment of the invention; 
           [0231]      FIG. 11D  is an illustration of example optical interface clamps, in accordance with embodiments of the invention; 
           [0232]      FIGS. 11E through 11G  are illustrations of an example optical interface mount, in accordance with an embodiment of the invention; 
           [0233]      FIG. 12A  is an illustration of an example mobile cart in accordance with an embodiment of the invention; 
           [0234]      FIG. 12B  is a photograph of an example mobile cart in accordance with an embodiment of the invention; 
           [0235]      FIG. 13  is a screenshot of a microscopy image acquired on fresh tissue using the disclosed technology. 
           [0236]      FIG. 14  is an image acquired on fresh mice kidney tissue using the disclosed technology. 
           [0237]      FIG. 15  shows a block diagram of an exemplary cloud computing environment; and 
           [0238]      FIG. 16  is a block diagram of a computing device and a mobile computing device. 
       
    
    
       [0239]    The features and advantages of the present disclosure will become more apparent from the detailed description set forth below when taken in conjunction with the drawings, in which like reference characters identify corresponding elements throughout. In the drawings, like reference numbers generally indicate identical, functionally similar, and/or structurally similar elements. 
       DETAILED DESCRIPTION OF THE INVENTION 
       [0240]    In the present text the expression “micro optical element” is used to describe a miniaturized focusing element with a cross sectional diameter of less than 1 mm (e.g., between 10 micrometers and 500 micrometers) that focuses light. In some implementations, the micro optical element is a micro lens having a paraxial radius of curvature that is in the order of magnitude of its diameter. In some implementations, the micro optical element is a refractive lens, Fresnel zone plate, GRIN lens, or micro reflective objective. The term “micro optical element array” is used to describe a structure composed of a plurality of micro optical elements positioned in a grid which may be, but is not necessarily, periodic. While the description may describe embodiments of the disclosed technology implemented with a micro lens array, similar embodiments may be implemented with micro optical elements. 
         [0241]    The expression “fresh tissue” is generally used herein to describe tissue resected or otherwise obtained during surgery that is not fixed tissue. For example, fresh tissue has not been frozen or processed with formalin, paraffin. In some implementations, the fresh tissue sample is in the same or similar state that it was in when it was removed from the patient. Fresh tissue is a living tissue that has not yet been fixed, in the histology terminology understanding. In the fields of histology and pathology, fixation is a critical step in the preparation of histological sections by which biological tissues are preserved from decay, thereby preventing autolysis or putrefaction. The broad objective of tissue fixation is to preserve cells and tissue components and to do this in such a way as to allow for the preparation of thin, stained sections. 
         [0242]    Even though the microscopy system described herein may be used to image fixed thin tissue sections, an advantage that is achieved, in certain embodiments, is to provide a solution for fresh tissue imaging that does not necessitate a fixation procedure and thin slicing of the sample. In consequence, embodiments described herein allow microscopic imaging on fresh thick tissue, in contrast to standard preparation of fixed thin tissue in histology. 
         [0243]    In the present text the expression “operating theatre” is used to describe a facility within a hospital where surgical operations are carried out in a sterile environment, including an operating room and operating suite. It also refers to an operating room with an on-site laboratory (e.g., adjacent to the operating room). In some implementations, the operating theatre is an operating room. 
         [0244]    The disclosed technology may be used for the observation of thick fresh tissue samples (e.g., having a thickness within a range of 0.5-20 mm, 3-5 mm, 5-10 mm, 7-15 mm, 10-25 mm, 15-30 mm, or 25-35 mm or is no less than 0.2 mm, no less than 0.5 mm, no less than 1 mm, no less than 3 mm, or no less than 5 mm)) at a cellular level during surgery in order to provide pathology assistance to ongoing surgery. The sample may be processed using the disclosed technology in less than 10 minutes (e.g., less than 5 mins) because, for example, the sample does not need to be mechanically sliced as the disclosed microscopy may be used directly on fresh thick tissue (e.g., using optical slicing, a non-destructive method). Further, the technical speed of reading the sample is improved, and this approach preserves the sample such that it is available for definitive assessment (contrary of FSA). Additionally, images can be shared electronically which allows direct connection between the pathologist and the surgical team. 
         [0245]      FIG. 1A  illustrates a top view of an example in-operating-theatre pathology system for imaging fresh, thick tissue.  FIG. 1B  illustrates a side view of the same example system. The disclosed technology uses a micro lens array  104  for performing large-field high resolution microscopy and/or micro-projection of in-operating-theatre imaging for fresh, thick tissue for pathology assessment. Fresh thick tissue is typically difficult to image as the illumination light is passed through the sample  101 , such as a biopsy or a tumor resection, and the collected emission light collected also travels through the sample  101 . The disclosed technology overcomes this challenge by using, among other things, transmitting optics to limit the part of the light path that has to propagate into the sample  101 , thereby allowing imaging of fresh thick tissue. Examples of transmitting optics that can be used include refractive lens, Fresnel zone plate and the micro reflective objective described in U.S. patent application Ser. No. 14/415,106, filed January 2015, entitled Reflective Optical Objective, which is hereby incorporated by reference in its entirety and attached hereto as an Appendix. 
         [0246]    The illumination light is provided by a light source  109  and is directed onto a beam splitter  112  that transmits the collected light. In some implementations, the illumination light is projected directly onto the beam splitter  112 . In other implementations, a flat mirror  111  redirects the illumination light onto the beam splitter  112 . 
         [0247]    In some implementations, a beam expander  110  (e.g., collimating lens) expands the waist of the illumination beam prior to the light reaching the beam splitter  112 , thereby providing an expanded illumination beam. In some implementations, the expanded illumination beam is projected directly onto the beam splitter  112 . In other implementations, a flat mirror  111  redirects the expanded illumination beam onto the beam splitter  112 . 
         [0248]    The beam splitter  112  reflects the illumination beam (i.e., the unexpanded illumination beam or expanded illumination beam depending on whether a beam expander is used) to a micro lens array  104 . In some implementations, the beam splitter  112  transmits the illumination beam to a micro lens array  104  via a flat mirror  105 . 
         [0249]    In some implementations, the beam splitter  112  separates light (e.g., reflects the illumination beams and allows the back-emitted light to pass therethrough) according to its wavelength, its polarization or without such distinctions. For example, a dichroic mirror or a polarizing cube associated with a quarter-wave, half-wave plate or a partially reflecting mirror can be used to achieve the desired effect. 
         [0250]    In some implementations, the system includes a micro lens array  104  that focuses the illumination beam onto a sample  101 . The illumination beam is focused by each of the micro lens, producing an array of foci in the sample  101 . The micro lens array  104  focuses the collimated light into the sample  101 , forming an array of tight foci in which fluorescence will be excited (e.g., fluorescence from the fluorescence stained sample  101 ). 
         [0251]    In some implementations, the micro lens array  104  includes plano-convex spherical lenses that focus the collimated beam of light. The plano-convex spherical lenses, in some implementations, are used with their curved surface facing the collimated beam in order to minimize aberrations (e.g., spherical aberrations). 
         [0252]    The same micro lens array  104  allows the light emitted from the sample  101  (i.e., back-emitted light) as a result of the illumination to pass ultimately towards a detector array  108 . The light emitted by the sample  101  in response to the illumination, in some implementations, is collected by each of the micro lens. In this example, the collected light then propagates as individual collimated beams. In some implementations, the flat mirror  105  reflects the back-emitted light to the beam splitter  112 . In contrast to the illumination beam which the beam splitter  112  reflects, the beam splitter  112  transmits the back-emitted light. 
         [0253]    After the back-emitted light passes through the beam splitter  112 , imaging optics  106  (e.g., field lens) focus the back-emitted light from the beam splitter  112  onto the detector  108 , thereby imaging the micro lens plane onto the detector plane. In some implementations, the back-emitted light from the beam splitter  112  is focused onto the detector  108  via an aperture stop  107  (e.g., pinhole). The aperture stop  107  spatially filters the light, thereby rejecting out-of-focus light. 
         [0254]    In some implementations, the light originating from each individual micro lens is independently detected by dedicated sensors element of the detector array  108 . The sensitive elements of the detector array  108  can be any type of sensor sensitive to the light collected by the micromirrors, such as CMOS or CCD photodetectors, photodiodes, phototransistors, avalanche photodiodes, photoresistors, Golay cells, bolometer thermopiles or pyroelectric detectors. 
         [0255]    Distances a and b as shown in  FIG. 1B  and the focal length of the relay optics can be chosen to arrange the magnification, therefore adapting the field of view such that the micro lens array  104  area maps onto the detector array  108  surface appropriately. This optical relay simultaneously allows spatial filtering for confocal detection when an aperture stop  107  is positioned in the Fourier plane of imaging optics  106 . In the example shown in  FIG. 2B , the focal length of the relay optics is 100 mm, distance a is 32 mm, and distance b is 100 mm. Other focal lengths and distances may be used as well. For example, the focal length may be between 70-130 mm, distance a may be between 20-50 mm and distance b may be between 80-102 mm. 
         [0256]    The relative motion between the sample  101  and the micro lens array  104  is achieved, in some implementations, with a scanning stage  103  that translates either the glass window on which the sample  101  sits or the micro lens array  104  (or both) in order to record variations of the sample signal with the changing position and to reconstruct an image therefrom. The camera  108  is recording the image plane situated at the back side of the micro lens array  104 . Therefore, every single micro lens signal is recorded simultaneously for a given position of the stage  103 . At a given position during the scanning process, multi-point information is recorded from the sample  101  and the relative position of all these point on the sample  101  is precisely known. By repeating this multi-point acquisition along the controlled scan pattern, the relative intensity variations recorded from each micromirror in the array in relation with their respective position on the sample  101  can be reconstructed by a computing device (e.g., a computing device integrated in the reader or separate from the reader). This provides the image of the sample  101  situated in the focal plane of the micro lens array  104 . 
         [0257]    If the sample  101  is situated partially outside of the focal plane of the micro lens array  104 , the signal intensity will drop in the corresponding region of the array. It gives topographic information of the distance separating the sample  101  from the focal plane of the micro lens array  104 . A particularly valuable use of this topographic information is the compensation of a tilt angle between the sample plane and the micro lens plane. A computer may be used to control the reading instrument, including image reconstruction and/or displaying the image. In some implementations, control and reconstruction is embedded in the reading device. 
         [0258]    In some implementations, the sample  101  is stained prior to processing using colored or fluorescent stains. For example, Proflavine, Acridine Orange, or other stains may be used. The staining procedure should remain simple to be executed in OR. For example, the staining procedure may comprise the steps: dip the tissue in a staining liquid, dip in a rinsing liquid, and then place the sample  101  on the glass above the micro lens array  104  for imaging. In certain embodiments, the sample  101  is placed in a sample holder  102  positioned above the micro lens array  104 . 
         [0259]      FIGS. 2A through 2C  are photographs of an example in-operating-theatre pathology system in accordance with an embodiment of the disclosed technology. This example system uses a micro lens array to perform large-field high resolution microscopy and/or micro-projection of fresh, thick tissue in an operating theatre for pathology assessment. The illumination light is provided by a light source  209  (e.g., laser) and expanded by a collimating lens  210  (e.g., a beam expander). The collimated light is then directed onto a beam splitter  212  by a flat mirror  211 . 
         [0260]    The beam splitter  212  reflects the illumination beam (i.e., the unexpanded illumination beam or expanded illumination beam depending on whether a beam expander is used) to a micro lens array via a flat mirror  205 . In this example, the beam splitter  212  is a dichroic mirror that separates light according to its wavelength (e.g., reflects the illumination beams and allows the collected fluorescence light to pass therethrough). 
         [0261]    A micro lens array (underneath the scanning stage  103  in this example) focuses the illumination beam onto a sample (not shown) on the sample holder  220 . The illumination beam is focused by each of the micro lens, producing an array of foci in the sample. The same micro lens array allows the light emitted from the sample (i.e., back-emitted light) as a result of the illumination to pass ultimately towards a detector array  208  (e.g., camera). The light emitted by the sample in response to the illumination is collected by each of the micro lens. In this example, the collected light then propagates as individual collimated beams. 
         [0262]    In some implementations, the flat mirror  205  reflects the back-emitted light to the beam splitter  212 . In contrast to the illumination beam which the beam splitter  212  reflects, the beam splitter  212  transmits the back-emitted light. After the back-emitted light passes through the beam splitter  212 , a field lens  206  focuses the back-emitted light from the beam splitter  212  onto the detector  208  via an aperture stop  207 , thereby imaging the micro lens plane onto the detector plane. The aperture stop  207  spatially filters the light, thereby rejecting out-of-focus light. 
         [0263]    In this example, the relative motion between the sample and the micro lens array is achieved with a scanning stage  203  (e.g., 3×20×20 cm) that translates in order to record variations of the sample signal with the changing position and to reconstruct an image therefrom. At a given position during the scanning process, the global surface topography of the sample can be reconstructed by comparing the relative intensity variations recorded from each micromirror in array. A particularly valuable use of this topographic information is the compensation of a tilt angle between the sample plane and the micromirror plane. In this example, a computer (not shown) is used to control the reading instrument, including image reconstruction and/or displaying the image. 
         [0264]    The system described in this example may be used for the observation of thick fresh tissue at a cellular level during surgery in order to provide pathology assistance to ongoing surgery. The sample may be processed using the disclosed technology in less than 10 minutes (e.g., less than 5 mins) using the system shown in  FIGS. 2A-C  in part because the sample does not need to be mechanically sliced as the disclosed microscopy may be used directly on fresh thick tissue (e.g., using optical slicing, a non-destructive method). Further, the pure technical speed of reading is improved and this approach preserves the sample such that it is available for definitive assessment (contrary of FSA). Additionally, images can be shared electronically which allows direct connection between the pathology and the surgery. 
         [0265]    In this example, the sample holder  220  includes a sample holder frame  222  that is attached to the scanning stage  203 . Specifically, in this example, the sample holder frame  222  is screwed to the scanning stage  203 , although other attachment systems may be used. The sample holder frame  222  has a this transparent window  224  onto which the tissue sample is deposited for imaging. In this example, the transparent window  224  is glass. 
         [0266]      FIG. 3  is an illustration of a method  300  for imaging thick fresh tissue in the operating theatre. A fresh tissue sample (e.g.,  101 ) is positioned on the glass window from the sample holder (e.g.,  102 ) (e.g., after fluorescent labeling process is applied to the sample  101 ) ( 302 ). In some implementations, the holder (e.g.,  102 ) is a metallic body (for cleaning or disinfection) with an opening window (e.g., 40×20 mm). The holder may be sealed at the bottom by a glass window for the instrument to be protected from liquid. In some implementations, the thin glass window secures an optical interface (transparent and flat) between the sample and the micro-optics chip. An example holder  220 , window, and scanning stage  203  is shown in  FIG. 2C . 
         [0267]    The holder, in some implementations, is designed specifically for this application. The tissue may be put in contact with a thin glass slide (e.g., 50-100 μm thick) and gently pressed against the glass slide to secure the contact over the area to be imaged. In some implementations, the holder is sealed for specific cases where the tissue needs to be immersed in a liquid for clinical reasons. In some implementations, the holder is used for the staining procedure. In other implementations, the holder is a metallic plate with a hole in its center and a glued thin glass slide on the bottom. 
         [0268]    In some implementations, the holder (e.g.,  102 ) is screwed on the scanning stage (e.g.,  103 ) ( 304 ). The stage, in some implementations, is a three-axis high precision positioning stage. The stage is used to bring the glass window in close proximity (e.g., &lt;100 um) to the chip (e.g.,  104 ). Then, the sample scan be imaged using the disclosed technology ( 306 ). 
         [0269]    The disclosed scanning microscopy allows for fast confocal imaging over large area. For example, the disclosed scanning microscopy can be designed with a larger micro lens array to increase the field of view. In comparison, confocal microscope traditionally uses a configuration with a microscope objective and beam scanning. The field of view is limited (500 μm-1 mm) by the objective and highly dependent on the chosen magnification. The beam scanning increases the acquisition time for each image compare to standard microscopy. Consequently, to cover a 20 mm field of view for instance, a standard motorized confocal microscope would need to aggregate 400 to 1600 images in this example. The disclosed technology increases the speed, flexibility of use, robustness, ergonomics and compactness thereby achieving an in-operating—room scanning microscopy for imaging thick fresh tissue. The parallel approach described herein allows the disclosed technology to cover the field of view (e.g., of 20 mm) with a scan range corresponding to the pitch of the array (e.g., of 0.25 mm) while a sequential approach forces the scan to cover the entire field of view ( 2  orders of magnitude larger) which limits the speed, flexibility of use robustness, ergonomics and compactness. 
         [0270]    In some implementations, the position of components in the system are fixed while only the sample is displaced (e.g., and in some implementations the scanning stage  103 ) by a translation fixture such that the sample may be scanned. In other implementations, the position of the sample relative to the system is fixed during scanning and the optical chip (e.g., micro lens array) is moved such that the sample is scanned. In this implementation, the image onto the detector will be moving, therefore the detected signal is processed to compensate for this movement. Further, in some implementations, the movement of the system during scanning is monitored to adjust the detected signal appropriately. Utilizing a moving optical chip rather than moving the sample itself while scanning eliminates any mobile component for the user to interact with and allows for a more robust external casing for cleaning and sterilization. 
         [0271]      FIGS. 4A-G  are illustrations of an example system for holding a sample. In this implementation, the sample holder is fixed and a mechanical translation stage moves the optical chip (e.g., micro lens array) relative to the rest of the system. In the example shown in  FIGS. 4A-G , the main structure is supported by a base  402  (e.g., 300 mm×300 mm) and additional pillars  404   a - c  (collectively  404 , post  404   d  not shown) (e.g., 100 mm tall). The global volume in this example is therefore 300 mm×300 mm×100 mm. Height may vary considering the height of the holding structure  406  for the sample (in purple here). Length may be increased (e.g., such that the camera is within the dimensions of the translation stage). Various dimensions may be used for the base  402  (e.g., width of 50 mm, 100 mm, 150 mm, 200 mm, or 250 mm, and lengths of 50 mm, 100 mm, 150 mm, 200 mm, or 250 mm, all values+/−50 mm) and the pillars  404  (e.g., 25 mm, 50 mm, or 75 mm, all values+/−25 mm). 
         [0272]    The optical path is below the base  402 , the scanning stage  408  is fixed on top of the base  402 . The mechanical structure (e.g.,  408  and  406 ) to hold the sample allows adjusting height and tilt of the sample relative to the stage and optical path. An optical window  410  (e.g., glass window) is located in the holding structure  406  such that a sample may be placed on the optical window  410  and a micro lens array positioned below the optical window  410  can focus light onto the sample and collect back-emitted light (e.g., fluorescence excited by the focused light) as described above. In some implementations, metal bars as shown in  FIGS. 4A-G  are provided such that the components of the system may be adjusted. In some implementations, the components are adjusted during manufacturing such that no further adjustments are necessary in the field. In other implementation, most of the adjustments are set during manufacturing, however, select fine adjustments may be made in the field. 
         [0273]    This example system uses a micro lens arrays to perform large-field high resolution microscopy and/or micro-projection of fresh, thick tissue in an operating theatre for pathology assessment. The illumination light is provided by a light source and expanded by a collimating lens (e.g., a beam expander). 
         [0274]    The beam splitter  414  reflects the illumination beam (i.e., the unexpanded illumination beam or expanded illumination beam depending on whether a beam expander is used) to a micro lens array via a flat mirror  416 . In this example, the beam splitter  414  is dichroic mirror that separates light according to its wavelength (e.g., reflects the illumination beams and allows the collected fluorescence light to pass therethrough). 
         [0275]    A micro lens array focuses the illumination beam onto a sample (not shown) on the sample holder. The illumination beam is focused by each of the micro lens, producing an array of foci in the sample. The same micro lens array allows the light emitted from the sample (i.e., back-emitted light) as a result of the illumination to pass ultimately towards a detector array  412 . The light emitted by the sample in response to the illumination is collected by each of the micro lens. In this example, the collected light then propagates as individual collimated beams. 
         [0276]    In some implementations, the flat mirror  416  reflects the back-emitted light to the beam splitter  414 . In contrast to the illumination beam which the beam splitter  414  reflects, the beam splitter  414  transmits the back-emitted light. After the back-emitted light passes through the beam splitter  414 , a field lens focuses the back-emitted light from the beam splitter  414  onto the detector  412  via an aperture stop, thereby imaging the micro lens plane onto the detector plane. The aperture stop spatially filters the light, thereby rejecting out-of-focus light. 
         [0277]      FIG. 5  is an illustration of an example sample holder system  500 . In this example, the sample holder  406  is a metallic part including a thin optical window  410 , which can be fixed on the system  500 . This illustrates an “all combined” solution where the glass window tilt and height relative to the scanning stage/optical chip (not shown) can be adjusted as a manufacturing setup, assuring that any sample deposited on the optical window  410  will be correctly positioned regarding the microscopy system to be imaged. 
         [0278]    For sterility constraints due to dedicated application in clinical use (e.g., operating theater), it may be preferable to include a single use element (e.g., a disposable element).  FIG. 6A  shows an example of such a single use element  600  that can be inserted in the system for each use. The sample holder may be used as an adaptive element to secure the single use element  600  on the system at the right position for imaging. The single use element  600 , in some implementations, includes a thin glass window  602  through which the imaging takes place. In some implementations, the element  600  includes a cover/lid  604  to protect the glass window  402  and enclose the sample once inserted into the body  606 . The element  600  provides axial positioning repeatability (e.g., mechanical tolerancing, in some implementations, is better than 10 μm (e.g., 1 to 10 μm)). In some implementations, the element  600  is stackable with other similar elements. For example, the body  606  can include feet  608   a - c  (foot  608   d  not shown). Additionally, the body  606  can include storage guides  610   a - d  that allow elements  600  to stack on top of each other easily. The storage guides  610   a - d  are spaced inside of corresponding feet  608   a - d  from another element  600  such that the guides  610   a - d  laterally secure elements  600  when they are stacked on one another. In some implementations, the element  600  includes prominent feet  608   a - c  (foot  608   d  not shown) to preserve optical interface when, for example, putting the element  600  on a dirty or damaging surface. 
         [0279]      FIGS. 6B and 6C  illustrate an additional sample holder  660  that can be used with an in-operating-theatre pathology system  662  (e.g., such as a system described herein). This example shows a system protected from environment (dust, liquid) by an external enclosure offering an opening window for imaging protected by a transparent material (such as glass). Such a system can be used for imaging without the sample holder  660  (e.g., disposable part), by directly placing the sample on the transparent window  654 . 
         [0280]    In the example shown in  FIGS. 6B and 6C , the system  662  is a closed system and the sample holder  660  rests/sits on top of a plate  654  (e.g., transparent; e.g., made of glass or a polymer) that itself is attached to the body  650  of the system. The optical array  652  is housed within the body  650 . For the purpose of this illustration, the entire body and system is not shown. As shown in  FIG. 6C , even when the sample holder  660  is removed the system  662  is closed and the optical array  652  is protected from the environment. However, such a system requires multiple, stacked up interfaces (e.g.,  654  and  660 ) and thus these interfaces must be thin and/or be optically transparent. In certain embodiments, the sample holder  660  is rigid, such as a polymer or glass. In other embodiments, the sample holder is flexible, such as a pellicle or film. 
         [0281]      FIGS. 6D and 6E  illustrate an additional sample holder  670  that can be use with an in-operating-theatre pathology system  672  (e.g., such as a system described herein). In this example, the system  672  is an open system as shown in  FIG. 6E  and the sample holder  670  (e.g., holder) rests, sits, or is attached to the body  650  of the system. The system is closed by a removable part  670 . The optical array  652  is housed within the body  650 . For the purpose of this illustration, the entire body and system is not shown. As shown in  FIG. 6E , even when the sample holder  670  is removed the system  672  is open and the optical array  652  is not protected from the environment. However, the optical interface is thinner and/or has improved optical transparency as the only interface is on the removable part  670 —there is no additional plate  654  as shown in  FIGS. 6B and 6C . 
         [0282]    The system shown in  FIGS. 6D and 6E  can includes a mounting system suited to accommodate the sample holder  670  (e.g., disposable sample holder) during an operation. In a surgical operation, for example, the tissue sample is placed on the sample holder  670  remotely from the system and then is brought to the system using the sample holder. In this example, the sample holder act as sample handler as well. The mounting system, in certain embodiments, has its own optical interface which is rigid to support tissue sample/specimen. 
         [0283]    The mounting system for the sample holder (e.g., such as the sample holder shown in  FIGS. 6A through 6E ) can be one of a variety of systems. For example, the mounting system for the sample holder can require no fixation—instead, the sample holder is simply deposited (e.g., placed) on the top side of the instrument in the appropriate position such that the sample holder sits or rests on top of the instrument. In other embodiments, the sample holder can be secured using an adhesive, mechanical fixation (e.g., screws, clamp or any locking device), or one or more magnets to hold the disposable in position. 
         [0284]      FIGS. 6F through 6J  illustrates one example for mounting a sample holder  690  to a pathology system. In this example, only the optical chip  652  portion of the pathology system is shown. In certain embodiments, a support base  680  can be mounted on the pathology system. The support base can include a mount  682  with one or more protrusions  684  extending from the mount  682 . In the example shown in  FIG. 6F , the support base  680  includes two protrusions  684 . The mount  682  is hollow on the inside and the support base  680  has a corresponding opening therein such that an optical chip  652  can scan a sample through the support base  680 . This embodiment includes a second piece, referred to as a removable sample holder  690 . The removable sample holder  690  includes a transparent window  692  through which the optical chip  652  can image a sample (e.g., the optical sensor is on one side of the transparent window  692  and the sample is on the opposite side of the transparent window  692 ). The removable sample holder  690  includes one or more interior protrusions  694 . In this example, the removable sample holder  690  includes two interior protrusions  694 . The width (labeled as  696  in  FIG. 61 ) of the vertical walls of the removable sample holder (excluding the interior protrusion(s)  694 ) is such that it can slide over the mount  682  when the protrusion(s)  684  and interior protrusion ( 694 ) are not aligned. Once the removable sample holder  694  is fully applied to the mount  682 , the removable sample holder  694  can be twisted (e.g., clockwise in this example) such that the protrusion(s)  684  and the interior protrusion(s)  694  are engaged with each other. This securely mates the removable sample holder  694  to the support base  680  such that the optical sensor  652  can image a sample placed on the transparent window  692  in the removable sample holder  694 . 
         [0285]      FIG. 7  is an illustration of an example kinematic structure that is used, in some implementations, for adjusting both height and tilt of the glass window (e.g., by moving the scanning stage) relative to the optical chip and corresponding optical path. In certain embodiments, the kinematic structure has three feet (although different numbers of feet may be used such as 2, 4, or 5) with adjustable height (micrometric screw—see  FIG. 7  kinematic base  700  holding the frame on which can be screwed the sample holder). The purpose of this kinematic base  700  is to adjust both height and tilt of the glass window (e.g., glass window  604  in  FIG. 6  or optical window  410  in  FIG. 4A ) relative to the optical chip (e.g., optical chip  902  in  FIG. 9  or micro lens array  104  in  FIG. 1A ) and corresponding optical path. The two surfaces (e.g., the glass window and the optical chip), in some implementations, have an area of about 20 mm by 20 mm (other dimensions may be used, such as a width of 10-60 mm and a length of 10-60 mm) and will be positioned at a close distance less than 500 μm (e.g., less than 400 μm, less than 300 μm, less than 200 μm, and/or greater than 100 μm, greater than 200, and/or between 100-200 μm, 200-300 μm, 300-400 μm, or 400-500 μm), which may require adjustment of these settings (e.g., during manufacturing). Additionally, the microscope performances are increased when all surfaces are positioned normal to the optical axis of the system. In the example shown in  FIG. 7 , the kinematic base  700  includes a magnet  706  (e.g., a pair of magnets may be used—a magnet in the seat  704  that is magnetically attracted to a magnet in the head  702 ) that exerts a force that aligns and maintains the head  702  in position on the seat  704 . The height and tilt is defined by the distance between head  702  and seat  704 , which is controlled with the adjuster screw  708  (e.g., ¼″-100). In an example that uses three kinematic feet, one kinematic foot may be screwed in to increase the distance between the respective seat  704  and head  702  and modify the global tilt and height of the platform standing on these feet. In this example, if all three kinematic feet are screwed with the same number of rotations, all feet height change the same way, which gives a pure platform height change. Otherwise, if the kinematic feet are not all screwed with the same number of rotations, the tilt is modified. 
         [0286]      FIG. 8  is an illustration of a camera  802  and pinhole  804  (e.g., aperture) assembly. The axial distance between the pinhole disk  804  (i.e., aperture stop) and the detector  802  (e.g., camera sensor) is determined from optics equations and is not extremely sensitive in terms of tolerances so it can be determined and mechanically set without the need for fine adjustment. Fine position, however, in certain embodiments, is required for the lateral position of the pinhole in the disk  804 . In certain embodiments, this requirement is provided using the system shown in  FIG. 8 . In  FIG. 8 , the position of the aperture stop relative to the optical axis is adjusted with an XY translating stage  806 , while the camera  802  has a fixed position relative to the optical axis. The aperture stop  804  (pinhole) is used to filter the collected light on a confocal manner before the light signal reaches the camera  802  sensor. The position of this aperture  804  is of importance as it selects the points of origin of the light collected in the sample. Adjusting this pinhole (i.e., small hole in the disk  804 ) position corresponds to adjusting the position of the grid of collected focal points in the sample. For maximizing the performance of the confocal microscope this collection grid must be aligned (match) with the illumination grid. This aperture  804  positioning is critical for correctly setting up the system. 
         [0287]    Also illustrated in  FIG. 8  is the optical interface clamp  808  (e.g.,  1108  shown in  FIG. 11D ). The optical interface clamp  808  is a ring-shaped part (although other shapes can be used) that maintains the optical interface  810  (e.g., transparent window) in place against the optical interface mount (e.g.,  1106  in  FIG. 11B ) and that seals the device with O-ring gaskets  812 . In certain embodiments, the optical interface clamp  1108  is designed to be in contact with the specimen while preventing the optical interface mount  1106  from contacting the specimen during use. 
         [0288]      FIG. 9  is an illustration of an example optical chip scanning system  900  that may be used with the optical system described above. In this example, the optical chip  902  is moved by a scanning system  904 . In the example shown in  FIG. 9 , the scanning system  904  and optical chip  902  are in an interior environment  950  of the instrument (e.g., fully or partially enclosed in the instrument) such that the optical chip  902  is protected from both the sample  906  and, in some implementations, outside environment  960  (i.e., outside of housing  910 ) by an optical (e.g., glass) window  908 . In some implementations, this allows for faster scan rates since the mass in motion is very small—in some implementations, the optical chip  902  weights from 0.5 to 2 grams (e.g., 0.9 to 1.1 grams, or 1 gram). 
         [0289]      FIGS. 10A-D  illustrate of an example system  1000  for in-operating-theatre imaging of fresh thick tissue resected during surgery for pathology assessment. In this example, a laser fiber  1002  (e.g., single mode optical fiber) provides laser light via a laser fiber output  1004 . The laser light is collimated by a collimating lens  1006  and then reflected off a dichroic beam splitter  1008  toward a beam steering mirror  1010  (e.g., at 45 degrees relative to the path of the collimated light). The beam steering mirror  1010  reflects the collimated laser beam upwards towards the optical chip  1012 . The optical chip (e.g., micro lens array) focuses the collimated light into the sample, forming an array of tight foci in which fluorescence will be excited (e.g., fluorescence from the fluorescence stained sample). 
         [0290]    In some implementations, as illustrated in  FIG. 10C , the micro lens array includes plano-convex spherical lenses that focus the collimated beam of light. The plano-convex spherical lenses, in some implementations, are used with their curved surface facing the collimated beam in order to minimize aberrations (e.g., spherical aberrations). However, in this implementation, the focal plane may not penetrate deep into the sample (e.g., only a 10-40 microns) since the focused light goes through the entire micro lens array substrate thickness, the separating medium (e.g., air), and the coverslip  1052  (e.g., glass). 
         [0291]    In some implementations, the plano-convex spherical lenses are used with their curved surface facing the sample as shown in  FIG. 10E . This allows the focal plane  1056  to penetrate much deeper into the sample (e.g., 100-500 microns). The optical elements (e.g., micro lenses  1014   a - 1014   k ) also collect and collimate fluorescence emission from the sample. The beam steering mirror  1010  reflects the collimated fluorescence emission horizontally toward the imaging lens  1016 . The imaging lens  1016  focuses the collimated fluorescence emission from each micro lens in the micro lens array  1012  through the common pinhole  1018  and forms an image of the micro lens array on the camera sensor  1020 . In terms of imaging, the camera sensor  1020  and the micro lens array  1012  form a pair of conjugate planes—the micro lens array  1012  is imaged on the camera sensor  1020  by the imaging lens  1016 . 
         [0292]      FIG. 10E  illustrates an example hyperbolic shape of the micro lenses  1014 .  FIG. 10F  illustrates an example system exciting the fluorescence in the sample with lens  1014   a - k  facing the sample.  FIG. 10G  illustrates the back-emitted light emitted by the excited fluorescence. 
         [0293]      FIG. 10E  illustrates an inverted configuration compared to  FIG. 10C . This configuration can provide a longer working distance at a cost of poorer optical performance. This drawback can be overcome by using optical elements with non-spherical curvature, such as conical curvature. In certain embodiments, the curvature of the optical elements is conical, hyperbolic, or parabolic, rather than spherical. The curvature can be described by the factor of conic constant k. 
         [0294]    In geometry, the conic constant k is a quantity describing conic sections. For negative k, the conic constant is given by the following equation: 
         [0000]        k=−e   2 , 
         [0295]    where e is the eccentricity of the conic section. The equation for a conic section with apex at the origin and tangent to the y axis is: 
         [0000]        y   2 −2 Rx +( k+ 1) x   2 =0
 
         [0296]    where k is the conic constant and R is the radius of curvature at x=0. This formulation is used in geometric optics to specify oblate elliptical (k&gt;0), spherical (k=0), prolate elliptical (0&gt;k&gt;−1), parabolic (k=−1), and hyperbolic (k&lt;−1) lens and mirror surfaces. When the paraxial approximation is valid, the optical surface can be treated as a spherical surface with the same radius. 
         [0297]    In certain embodiments, the conic constant k is a negative value with absolute value greater or equal to 0.5. A typical range for k is −10&lt;k&lt;−0.8. In certain embodiments, the range for k is −3&lt;k&lt;−0.9. 
         [0298]    For example, an optical elements having radius of curvature of 195 um plus or minus 5 μm can be used. For example, optical elements having a radius of curvature from 190 μm to 200 μm, with a conicity k=−2.0 provides the following desired range of property values: Strehl ratio: 0.9&lt;S&lt;1, glass thickness for the sample interface  1052 : 300 um+/−100 um; air gap  1057  between optical chip  1051  and glass interface  1052  from 150+/−50 um; and/or depth of imaging plane  1056  inside the sample  1055  of 50 um+/−50 um. Other combinations of radius of curvature and/or conicities can be chosen to produce optical elements providing properties within these desired ranges for performing the functions described herein. 
         [0299]    The shape of the optical elements may vary. For example, in certain embodiments, each micro optical element has a conical shaped surface. In certain embodiments, each micro optical element has a hyperbolic shaped surface. In certain embodiments, the curved surface of each micro optical element has a conic constant k from −1.8 to −2.2 (e.g., −2). In certain embodiments, each micro optical element has a Strehl ratio greater than or equal to 0.8. Furthermore, in certain embodiments, each micro optical element has a spot size from 0.2 μm to 5 μm, 0.2 μm to 1 μm, 0.3 μm to 0.6 μm, 0.4 μm to 0.5 μm, greater than or equal to 0.2, and less than or equal to 5 μm. The system can have a free working distance (i.e., a distance from the tip of the micro optical elements to a focal plane of the micro optical element array) from 80 μm to 450 μm, 150 μm to 350 μm, or 250 μm to 300 μm. Additionally, the resulting focal plane of the micro optical element array can be from 10 μm to 200 μm, 20 μm to 150 μm, or 50 μm to 100 μm above the transparent window (i.e., the depth of the focal plane into a sample being imaged). 
         [0300]    As shown in  FIG. 10E , the curved surfaces of the lenses  1014  are facing the glass interface  1052  with the sample  1055  thereon. The curvature is chosen to optimize optical performance and working distance. The quality criteria for optical performance is to minimize optical aberration at the focal plane. A way of evaluating this quality is the Strehl ratio. The Strehl ration has a value between zero and one, an unaberrated optical system attaining the value of unity. Compared to  FIG. 10C , the inverted configuration of  FIG. 10E  increases the working distance which allows the use of a thicker glass interface  1052  and improves safety in the operating room. 
         [0301]    In certain embodiments, as shown in  FIG. 10E , the areas (e.g., flat areas) in between micro-lenses  1014  are covered by an absorptive and/or reflective layer  1054 . This layer  1054  can be, for example, a chromium layer, aluminum layer, or dielectric mirror layer. The purpose of this layer is to prevent or minimize the amount of illumination light transmitted by the optical chip that would travel outside of the system and possibly reach the eye of the operator. This can improve the safety of the system. The flat surface is covered because the illumination beam is collimated and therefore can travel long distance if not deviated by the curved surface. For the part of the beam focused by the curved surface, the beam is highly diverging at the distance of operator eyes which, when correctly designed, drastically diminishes the power received to a safe level. 
         [0302]    The system disclosed herein provides several benefits. For example, alignment of the micro lens array axis with the scanning stage axis is robust. The micro lens array may be aligned by hand within approximately 5 degrees and a small rotation can be compensated for by software with a proper calibration routine for allocation of camera pixels to the optical element, offsetting, and/or rotating tiles during image reconstruction. 
         [0303]    Misalignment between the micro lens array axis with camera axis can be compensated for by software, with a pixel allocation layer for arbitrary attribution of the camera pixels to the optical element. Similarly, alignment of the scanning stage axis with the camera axis in the embodiment in which the micro lens array is moved for scanning can be compensated for by software with a proper calibration routine and subsequent allocation of camera pixels to optical element. 
         [0304]    Lateral alignment of confocal pinhole with the imaging lens must be precise. The pinhole will be relatively small (e.g., 75-400 μm) and must be precisely aligned in the imaging lens focal plane. This may be accomplished, for example, using an XY micrometer. The axial alignment of the confocal pinhole with the imaging lens is also important. For relatively long focal length of the imaging lens (e.g., f&gt;50 mm), alignment in Z direction is not as critical and can be accomplished within 1 mm or better without precise positioning system. 
         [0305]    The axial positioning of the imaging lens from the micro lens array plane determines the magnification of the imaging system. In some implementations, this does not need to be precisely adjusted. 
         [0306]    The axial positioning of the imaging lens from the camera sensor plane determines how well focused the image of the micro lens array is on the camera sensor. In some implementations, considering the effective resolution of the imaging system through the confocal pinhole, manual adjustment of the lens position (e.g., to within 1 mm) on the cage system is sufficient for the long focal length of the imaging lens (e.g., f&gt;50 mm). Further, for a long focal length imaging lens (e.g., f&gt;50 mm), the axial positioning of pinhole from camera sensor plane, in some implementations, must be within less than or equal to a millimeter. For long focal length of the collimating lens (e.g., f&gt;50 mm), which are needed to generate large beam diameter to illuminate the full micro lens array, manual adjustment of the axial positioning of the fiber collimation lens (e.g., to 1 mm) on the cage system is sufficient. 
         [0307]    For a collimation of fibered light source, the lateral position of the fiber collimation lens is critical. A XY micrometer, for example, may be used to center optical fiber on collimating lens optical axis. 
         [0308]    In scanning microscopy, the resolution of the image may depend on the position of the reader while scanning the sample. In some implementations, the image is reconstructed based on the relation between the position of the reader relative to the sample and the corresponding signal measured by the detector. Image quality may be deteriorated by imprecise position measurement. In some implementations, positioning feedback is accomplished using a closed loop positioning system to compensate for non-linearity, hysteresis and drift issues. 
         [0309]    In some implementations, focusing elements may be used for positioning feedback. For example, one or more micro lenses can be used to record the image of a local known pattern, thereby providing a two or three-dimensional position feedback. In some implementations, the achromatic property of the lens allows for using a different wavelength for the feedback than the one used to image the sample. This allows image information to be easily separated from the positioning information with a dichroic beam splitter. 
         [0310]    As described above in relation to  FIG. 4  and  FIG. 5 , the disclosed technology, in certain embodiments, includes a sample holder. In some embodiments, the disclosed technology also includes a kinematic support. In certain embodiments, the specimen imaging interface designates the part of the assembly on which the specimen is imaged. 
         [0311]      FIGS. 11A through 11G  illustrate an example implementation of a specimen imaging area in accordance with an embodiment of the disclosed technology. In this example, the design is optimized to take into account requirements for use in hospital and ergonomic integration in the operating room workflow. The system is designed to be robust to fluid leakage. In particular, it includes a containment ring sealed on the glass window to prevent liquid related to the sample from being in contact with the rest of the device (e.g., for safety—hygiene). Additionally, the design minimizes the risk of liquid flowing inside the device during the cleaning of the device (efficacy). 
         [0312]      FIGS. 11A and 11B  illustrate an example specimen imaging interface on the microscopy instrument.  FIG. 11A  illustrates the specimen imaging interface  1100  connected to the rest of the imaging system  1190  whereas  FIG. 11B  illustrates the specimen imaging interface  1100  alone. The optical interface  1102  is the surface on which the specimen lies. It protects the optical chip  1104  and the rest of the instrument from the environment (dust, liquids, etc. including the specimen itself). It is compatible with the imaging process (transparency, planarity, etc.). 
         [0313]    The optical interface mount  1106  is the mechanical support for the optical interface  1102 . The optical interface clamp  1108  is the ring-shaped part (although other shapes can be used) that maintains the optical interface  1102  (e.g., transparent window) in place against the optical interface mount  1106 . The optical interface clamp  1108  seals the device with O-ring gaskets (not shown). In certain embodiments, the optical interface clamp  1108  is designed to be in contact with the specimen while preventing the optical interface mount  1106  from contacting the specimen during use. 
         [0314]    The kinematic blocks  1112  serve to mount the precision adjusters  1114  which form the basis of the kinematic system. In certain embodiments, the kinematic system is a three-point kinematic system that uses only three adjusters for kinematic positioning of the optical interface mount  1106 . In other embodiments, the kinematic system is a four-point kinematic system that uses four adjusters. Other variations are possible as well. Additionally, the kinematic blocks  1112  serve to mount the protective plates that delimit the perimeter of the specimen imaging interface, and protect sensitive components located under the optical interface mount  1106  from the outside environment. The top of the adjusters  1114  on each kinematic block  1112  contact at least a portion of a respective groove  1154   a - d  (collectively  1154 ) on the bottom side of the optical interface mount  1106  such that the grooves  1154  on the bottom side of the optical interface mount  1106  each sit on a respective kinematic block  1112  as shown in  FIGS. 11E and 11F . 
         [0315]    The base plate/frame refers to the mechanical backbone of the instrument on which all the components and modules are fixed. The baseplate is not part of the specimen imaging interface. 
         [0316]    As illustrated in  FIG. 11C , the entire optical interface mount assembly (with optical interface  1102 , optical interface clamp  1108 , etc.) can be magnetically maintained in position on the kinematic system and can be removed easily. Removing the optical interface mount  1106  exposes sensitive components (notably the optical chip  1104  and the scanning stage) to the “outside” environment (dust, liquid spill, mechanical impact, etc.) and allows removal of the optical interface  1102  itself. In this example, as shown in  FIG. 11C , the optical interface clamp  1108  is fastened by five screws and can thus be removed relatively easily to allow replacement of the optical interface  1102  or the O-ring seals. Other attachment systems or numbers of screws can be used to fasten the optical interface clamp  1108  to the system. 
         [0317]    The optical interface mount  1106  sits on the precision adjusters  1114  (e.g., three precision adjusters  1114 ) of the kinematic system. The position of the optical interface mount  1106  can be maintained by magnets. The optical interface mount  1106  can thus be easily removed from the microscopy instrument. In the example shown in  FIG. 11A through 11C , the optical interface mount  1106  is machined from a 200 mm×200 mm×8 mm aluminum plate and has a anodized finish. 
         [0318]    In certain embodiments, the optical interface clamp  1108  has two hidden grooves that accommodate O-rings to seal off the device by (i) preventing liquids inside the ring  1108  from flowing into the device, and (ii) preventing liquid spilled outside the ring  1108  from flowing into the device.  FIG. 11D  illustrates two examples of optical interface clamps  1108 . In both of these examples, the optical interface clamp  1108  is fastened to the optical interface mount  1106  by hardware  1010 , such as countersunk flat head screws. In this example, the optical interface clamp  1108  and optical interface  1102  can be disposable or sterilizable. The optical interface clamp  1108  can secure the optical interface  1102  onto the system and seal against the optical interface  1102  and/or optical interface mount  1106  to prevent liquid leakage from the sample into the system. 
         [0319]      FIGS. 11E through 11G  illustrate an example of a spill-proof optical interface mount  1106 . Specifically,  FIG. 11E  is a top view of the optical interface mount  1106  showing the groove  1152   a - d  (collectively groove  1152 ) in the bottom of the optical interface mount  1106 .  FIG. 11F  is a bottom view of the example spill-proof optical interface mount  1106  and  FIG. 11G  is a cross-sectional view of the example spill-proof optical interface mount  1106  along section A-A as shown in  FIG. 11F . It is important, in certain embodiments, to prevent liquid spilled on the optical interface mount  1106  from flowing into the device. In this example, the bottom surface of the optical interface mount  1106  near the perimeter of the optical interface mount  1006  is has a groove  1152  (e.g., a groove with a rectangular, circular, oval, triangular, or square cross-section) that prevents droplets on the bottom surface from migrating inwards). If liquid drains off the edge of the top surface of the interface mount  1106 , it will fall down when it reaches the groove  1152 . This prevents or reduces the likelihood that the liquid enters the system under the optical interface mount  1106 . 
         [0320]      FIG. 12A  is an illustration of an example mobile cart with an imaging device thereon for providing in-operating-theatre imaging of fresh thick tissue resected during surgery for pathology assessment and  FIG. 12B  is a photograph of an example of such a mobile cart. 
         [0321]    As shown in  FIG. 12A , an example mobile cart  1200  may include a plurality (e.g., three or four) wheels  1209  on which the cart can be rolled. Other transportation systems may be used as well, such as tracks. The cart  1200  can be motorized or can be pulled/pushed by a user. The mobile cart includes a microscopy instrument  1210 , such as the instrument described herein, with a specimen imaging interface  1212 . In certain embodiments, the mobile cart  1200  includes a display monitor  1205 , a keyboard,  1206 , and a user interaction device  1207  (e.g., touch pad, touch screen on the display monitor  1205 , and/or computer mouse). The microscopy instrument  1210  can be connected to the display monitor  1205  such that scans/images of the specimen in the imaging area  1213  can be shown on the display monitor  1206 . 
         [0322]    In certain embodiments, the cart includes handles, such as a front side handle  1211  and backside handles  1210 . The mobile cart  1200  can be equipped with a power switch  1201  (e.g., on/off switch) that is used to control power to equipment on the mobile cart  1200 . A power cable  1203  can be used to connect the mobile cart  1200  to a power source. In certain embodiments, the cart  1200  has a battery for self-sufficient use. The mobile cart  1200  can also include an equipotential bonding cable  1204 . The mobile cart  1200  can include one or more drawers  1208  (e.g., two drawers as shown in  FIG. 12A ). The mobile cart  1200  can also include a cable winder  1202  around which one or more cables can be wound for storage during, before, or after use. 
         [0323]    Experiments 
         [0324]    Several experiments were performed to identify sufficient optical chip designs. In these experiments, optical chip designs were tested using different curvature lenses and different lens orientations. Specifically, the lens orientation varied from facing the illumination beam and facing the sample. The shape of the lenses varied from spherical to conical. Table 1 summarizes the test results by showing the main quality criteria evaluated along with the tested optical chip configurations and curvature shapes. 
         [0000]    
       
         
               
               
               
               
             
               
               
               
             
               
               
               
             
               
             
               
               
               
               
             
           
               
                 TABLE 1 
               
               
                   
               
               
                 Optical Chip Design 
                 1 
                 2 
                 3 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 Configuration 
                 A 
                 B 
               
             
          
           
               
                 Curvature shape 
                 Spherical 
                 Conical (k = −2.0) 
               
             
          
           
               
                 Performance criteria 
               
             
          
           
               
                 fWD (um) 
                 110 
                 420 
                 400 
               
               
                 Spot size 
                    2.1 
                   11.6 
                    0.34 
               
               
                 RMS radius (um) 
               
               
                 Performance for 
                 Lower 
                 Poor 
                 High 
               
               
                 microscopy 
                 performance; 
                 Performance; 
                 Performance; 
               
               
                   
                 lower 
                 out of 
                 best 
               
               
                   
                 specification 
                 specification 
                 specification 
               
               
                 Strehl ratio 
                 &lt;0.8 
                 &lt;0.8 
                 0.91 
               
               
                 level of 
                 aberrated 
                 aberrated 
                 diffraction 
               
               
                 aberration 
                 optics 
                 optics 
                 limited 
               
               
                   
               
             
          
         
       
     
         [0325]    In these experiments, three optical chips designs were tested. The optical chip design of configuration A utilized lenses having a curvature facing the illumination beam. In contrast, the optical chip designs of configuration B utilized lenses having a curvature facing the sample. Optical chip designs 1 and 2 utilized spherical lenses as described above while chip design 3 utilized conical lenses as described above. The optimization aims to maximize the free working distance (fWD) while minimizing the spot radius and maintaining high performance microscopy. The spot radius is representative of the smallest detail that can be distinguished by the optical system, hence it relates to resolution. Thus, optimization aims at minimizing the spot radius value. The Strehl ratio is a way of quantifying the level of aberration. Being diffraction limited means that the system reaches the physical limits and can therefore be considered as a non-aberrated optical system. 
         [0326]      FIG. 13  is a screenshot of a microscopy image of fresh tissue acquired using the disclosed technology, specifically using optical chip design 3 from Table 1. The screenshot shows the Graphical User Interface (GUI), the alignment marks (e.g. square, triangle and round) to recognize tissue orientation, and the image obtained with a fresh porcine eyelid tissue deposited on the scanner instrument. The disclosed technology was used to capture an image that represents a digital slice of the fresh tissue—thus, allowing an image of a cross section of the tissue to be taken without actually slicing the tissue. 
         [0327]      FIG. 14  is an image acquired on fresh mice kidney tissue (i.e., the piece of tissue has been deposited on the instrument). The insert in the image shows a zoomed adipose tissue region and illustrates that the whole image is not showed at full resolution and can be zoomed to reveal further details with appropriate software display tool. Again, the disclosed technology was used to capture an image that represents a digital slice of the fresh tissue—thus, allowing an image of a cross section of the tissue to be taken without actually slicing the tissue. 
         [0328]    As shown in  FIG. 15 , an implementation of a network environment  1500  for use providing in-operating-theatre imaging of fresh thick tissue resected during surgery for pathology assessment is shown and described. In brief overview, referring now to  FIG. 15 , a block diagram of an exemplary cloud computing environment  1500  is shown and described. The cloud computing environment  1500  may include one or more resource providers  1502   a ,  1502   b ,  1502   c  (collectively,  1502 ). Each resource provider  1502  may include computing resources. In some implementations, computing resources may include any hardware and/or software used to process data. For example, computing resources may include hardware and/or software capable of executing algorithms, computer programs, and/or computer applications. In some implementations, exemplary computing resources may include application servers and/or databases with storage and retrieval capabilities. Each resource provider  1502  may be connected to any other resource provider  1502  in the cloud computing environment  1500 . In some implementations, the resource providers  1502  may be connected over a computer network  1508 . Each resource provider  1502  may be connected to one or more computing device  1504   a ,  1504   b ,  1504   c  (collectively,  1504 ), over the computer network  1508 . 
         [0329]    The cloud computing environment  1500  may include a resource manager  1506 . The resource manager  1506  may be connected to the resource providers  1502  and the computing devices  1504  over the computer network  1508 . In some implementations, the resource manager  1506  may facilitate the provision of computing resources by one or more resource providers  1502  to one or more computing devices  1504 . The resource manager  1506  may receive a request for a computing resource from a particular computing device  1504 . The resource manager  1506  may identify one or more resource providers  1502  capable of providing the computing resource requested by the computing device  1504 . The resource manager  1506  may select a resource provider  1502  to provide the computing resource. The resource manager  1506  may facilitate a connection between the resource provider  1502  and a particular computing device  1504 . In some implementations, the resource manager  1506  may establish a connection between a particular resource provider  1502  and a particular computing device  1504 . In some implementations, the resource manager  1506  may redirect a particular computing device  1104  to a particular resource provider  1102  with the requested computing resource. 
         [0330]      FIG. 16  shows an example of a computing device  1600  and a mobile computing device  1650  that can be used to implement the techniques described in this disclosure. The computing device  1600  is intended to represent various forms of digital computers, such as laptops, desktops, workstations, personal digital assistants, servers, blade servers, mainframes, and other appropriate computers. The mobile computing device  1650  is intended to represent various forms of mobile devices, such as personal digital assistants, cellular telephones, smart-phones, and other similar computing devices. The components shown here, their connections and relationships, and their functions, are meant to be examples only, and are not meant to be limiting. 
         [0331]    The computing device  1600  includes a processor  1602 , a memory  1604 , a storage device  1606 , a high-speed interface  1608  connecting to the memory  1604  and multiple high-speed expansion ports  1610 , and a low-speed interface  1612  connecting to a low-speed expansion port  1614  and the storage device  1606 . Each of the processor  1602 , the memory  1604 , the storage device  1606 , the high-speed interface  1608 , the high-speed expansion ports  1610 , and the low-speed interface  1612 , are interconnected using various busses, and may be mounted on a common motherboard or in other manners as appropriate. The processor  1602  can process instructions for execution within the computing device  1600 , including instructions stored in the memory  1604  or on the storage device  1606  to display graphical information for a GUI on an external input/output device, such as a display  1616  coupled to the high-speed interface  1608 . In other implementations, multiple processors and/or multiple buses may be used, as appropriate, along with multiple memories and types of memory. Also, multiple computing devices may be connected, with each device providing portions of the necessary operations (e.g., as a server bank, a group of blade servers, or a multi-processor system). 
         [0332]    The memory  1604  stores information within the computing device  1600 . In some implementations, the memory  1604  is a volatile memory unit or units. In some implementations, the memory  1604  is a non-volatile memory unit or units. The memory  1604  may also be another form of computer-readable medium, such as a magnetic or optical disk. 
         [0333]    The storage device  1606  is capable of providing mass storage for the computing device  1600 . In some implementations, the storage device  1606  may be or contain a computer-readable medium, such as a floppy disk device, a hard disk device, an optical disk device, or a tape device, a flash memory or other similar solid state memory device, or an array of devices, including devices in a storage area network or other configurations. Instructions can be stored in an information carrier. The instructions, when executed by one or more processing devices (for example, processor  1602 ), perform one or more methods, such as those described above. The instructions can also be stored by one or more storage devices such as computer- or machine-readable mediums (for example, the memory  1604 , the storage device  1606 , or memory on the processor  1602 ). 
         [0334]    The high-speed interface  1608  manages bandwidth-intensive operations for the computing device  1600 , while the low-speed interface  1612  manages lower bandwidth-intensive operations. Such allocation of functions is an example only. In some implementations, the high-speed interface  1608  is coupled to the memory  1604 , the display  1616  (e.g., through a graphics processor or accelerator), and to the high-speed expansion ports  1610 , which may accept various expansion cards (not shown). In the implementation, the low-speed interface  1612  is coupled to the storage device  1606  and the low-speed expansion port  1614 . The low-speed expansion port  1614 , which may include various communication ports (e.g., USB, Bluetooth®, Ethernet, wireless Ethernet) may be coupled to one or more input/output devices, such as a keyboard, a pointing device, a scanner, or a networking device such as a switch or router, e.g., through a network adapter. 
         [0335]    The computing device  1600  may be implemented in a number of different forms, as shown in the figure. For example, it may be implemented as a standard server  1620 , or multiple times in a group of such servers. In addition, it may be implemented in a personal computer such as a laptop computer  1622 . It may also be implemented as part of a rack server system  1624 . Alternatively, components from the computing device  1600  may be combined with other components in a mobile device (not shown), such as a mobile computing device  1650 . Each of such devices may contain one or more of the computing device  1600  and the mobile computing device  1650 , and an entire system may be made up of multiple computing devices communicating with each other. 
         [0336]    The mobile computing device  1650  includes a processor  1652 , a memory  1664 , an input/output device such as a display  1654 , a communication interface  1666 , and a transceiver  1668 , among other components. The mobile computing device  1650  may also be provided with a storage device, such as a micro-drive or other device, to provide additional storage. Each of the processor  1652 , the memory  1664 , the display  1654 , the communication interface  1666 , and the transceiver  1668 , are interconnected using various buses, and several of the components may be mounted on a common motherboard or in other manners as appropriate. 
         [0337]    The processor  1652  can execute instructions within the mobile computing device  1650 , including instructions stored in the memory  1664 . The processor  1652  may be implemented as a chipset of chips that include separate and multiple analog and digital processors. The processor  1652  may provide, for example, for coordination of the other components of the mobile computing device  1650 , such as control of user interfaces, applications run by the mobile computing device  1650 , and wireless communication by the mobile computing device  1650 . 
         [0338]    The processor  1652  may communicate with a user through a control interface  1658  and a display interface  1656  coupled to the display  1654 . The display  1654  may be, for example, a TFT (Thin-Film-Transistor Liquid Crystal Display) display or an OLED (Organic Light Emitting Diode) display, or other appropriate display technology. The display interface  1656  may comprise appropriate circuitry for driving the display  1654  to present graphical and other information to a user. The control interface  1658  may receive commands from a user and convert them for submission to the processor  1652 . In addition, an external interface  1662  may provide communication with the processor  1652 , so as to enable near area communication of the mobile computing device  1650  with other devices. The external interface  1662  may provide, for example, for wired communication in some implementations, or for wireless communication in other implementations, and multiple interfaces may also be used. 
         [0339]    The memory  1664  stores information within the mobile computing device  1650 . The memory  1664  can be implemented as one or more of a computer-readable medium or media, a volatile memory unit or units, or a non-volatile memory unit or units. An expansion memory  1674  may also be provided and connected to the mobile computing device  1650  through an expansion interface  1672 , which may include, for example, a SIMM (Single In Line Memory Module) card interface. The expansion memory  1674  may provide extra storage space for the mobile computing device  1650 , or may also store applications or other information for the mobile computing device  1650 . Specifically, the expansion memory  1674  may include instructions to carry out or supplement the processes described above, and may include secure information also. Thus, for example, the expansion memory  1674  may be provide as a security module for the mobile computing device  1650 , and may be programmed with instructions that permit secure use of the mobile computing device  1650 . In addition, secure applications may be provided via the SIMM cards, along with additional information, such as placing identifying information on the SIMM card in a non-hackable manner. 
         [0340]    The memory may include, for example, flash memory and/or NVRAM memory (non-volatile random access memory), as discussed below. In some implementations, instructions are stored in an information carrier. that the instructions, when executed by one or more processing devices (for example, processor  1652 ), perform one or more methods, such as those described above. The instructions can also be stored by one or more storage devices, such as one or more computer- or machine-readable mediums (for example, the memory  1664 , the expansion memory  1674 , or memory on the processor  1652 ). In some implementations, the instructions can be received in a propagated signal, for example, over the transceiver  1668  or the external interface  1662 . 
         [0341]    The mobile computing device  1650  may communicate wirelessly through the communication interface  1666 , which may include digital signal processing circuitry where necessary. The communication interface  1666  may provide for communications under various modes or protocols, such as GSM voice calls (Global System for Mobile communications), SMS (Short Message Service), EMS (Enhanced Messaging Service), or MMS messaging (Multimedia Messaging Service), CDMA (code division multiple access), TDMA (time division multiple access), PDC (Personal Digital Cellular), WCDMA (Wideband Code Division Multiple Access), CDMA2000, or GPRS (General Packet Radio Service), among others. Such communication may occur, for example, through the transceiver  1668  using a radio-frequency. In addition, short-range communication may occur, such as using a Bluetooth®, Wi-Fi™, or other such transceiver (not shown). In addition, a GPS (Global Positioning System) receiver module  1670  may provide additional navigation- and location-related wireless data to the mobile computing device  1650 , which may be used as appropriate by applications running on the mobile computing device  1650 . 
         [0342]    The mobile computing device  1650  may also communicate audibly using an audio codec  1660 , which may receive spoken information from a user and convert it to usable digital information. The audio codec  1660  may likewise generate audible sound for a user, such as through a speaker, e.g., in a handset of the mobile computing device  1650 . Such sound may include sound from voice telephone calls, may include recorded sound (e.g., voice messages, music files, etc.) and may also include sound generated by applications operating on the mobile computing device  1650 . 
         [0343]    The mobile computing device  1650  may be implemented in a number of different forms, as shown in the figure. For example, it may be implemented as a cellular telephone  1680 . It may also be implemented as part of a smart-phone  1682 , personal digital assistant, or other similar mobile device. 
         [0344]    Various implementations of the systems and techniques described here can be realized in digital electronic circuitry, integrated circuitry, specially designed ASICs (application specific integrated circuits), computer hardware, firmware, software, and/or combinations thereof. These various implementations can include implementation in one or more computer programs that are executable and/or interpretable on a programmable system including at least one programmable processor, which may be special or general purpose, coupled to receive data and instructions from, and to transmit data and instructions to, a storage system, at least one input device, and at least one output device. 
         [0345]    These computer programs (also known as programs, software, software applications or code) include machine instructions for a programmable processor, and can be implemented in a high-level procedural and/or object-oriented programming language, and/or in assembly/machine language. As used herein, the terms machine-readable medium and computer-readable medium refer to any computer program product, apparatus and/or device (e.g., magnetic discs, optical disks, memory, Programmable Logic Devices (PLDs)) used to provide machine instructions and/or data to a programmable processor, including a machine-readable medium that receives machine instructions as a machine-readable signal. The term machine-readable signal refers to any signal used to provide machine instructions and/or data to a programmable processor. 
         [0346]    To provide for interaction with a user, the systems and techniques described here can be implemented on a computer having a display device (e.g., a CRT (cathode ray tube) or LCD (liquid crystal display) monitor) for displaying information to the user and a keyboard and a pointing device (e.g., a mouse or a trackball) by which the user can provide input to the computer. Other kinds of devices can be used to provide for interaction with a user as well; for example, feedback provided to the user can be any form of sensory feedback (e.g., visual feedback, auditory feedback, or tactile feedback); and input from the user can be received in any form, including acoustic, speech, or tactile input. 
         [0347]    The systems and techniques described here can be implemented in a computing system that includes a back end component (e.g., as a data server), or that includes a middleware component (e.g., an application server), or that includes a front end component (e.g., a client computer having a graphical user interface or a Web browser through which a user can interact with an implementation of the systems and techniques described here), or any combination of such back end, middleware, or front end components. The components of the system can be interconnected by any form or medium of digital data communication (e.g., a communication network). Examples of communication networks include a local area network (LAN), a wide area network (WAN), and the Internet. 
         [0348]    The computing system can include clients and servers. A client and server are generally remote from each other and typically interact through a communication network. The relationship of client and server arises by virtue of computer programs running on the respective computers and having a client-server relationship to each other. 
         [0349]    Components described herein may be made of polymer, metal, metalloid, glass, ceramic, or other materials, or composites thereof. In certain embodiments, components are made of surgical grade materials. Components may be sterilizable, autoclavable, reusable, and/or disposable. Disposable components may be designed for single use or limited multi-use (e.g., between 2 and 10 uses). 
         [0350]    In view of the structure, functions and apparatus of the systems and methods described here, in some implementations, a system and method for providing in-operating-theatre imaging of fresh thick tissue resected during surgery for pathology assessment are provided. Having described certain implementations of methods and apparatus for supporting in-operating-theatre imaging of fresh thick tissue resected during surgery for pathology assessment, it will now become apparent to one of skill in the art that other implementations incorporating the concepts of the disclosure may be used. Therefore, the disclosure should not be limited to certain implementations, but rather should be limited only by the spirit and scope of the following claims. 
         [0351]    Having described certain implementations of methods and apparatus for supporting transfer printing capacitors, it will now become apparent to one of skill in the art that other implementations incorporating the concepts of the disclosure may be used. Therefore, the disclosure should not be limited to certain implementations, but rather should be limited only by the spirit and scope of the following claims. 
         [0352]    Throughout the description, where apparatus and systems are described as having, including, or comprising specific components, or where processes and methods are described as having, including, or comprising specific steps, it is contemplated that, additionally, there are apparatus, and systems of the disclosed technology that consist essentially of, or consist of, the recited components, and that there are processes and methods according to the disclosed technology that consist essentially of, or consist of, the recited processing steps. 
         [0353]    It should be understood that the order of steps or order for performing certain action is immaterial so long as the disclosed technology remains operable. Moreover, two or more steps or actions may be conducted simultaneously.