Patent Publication Number: US-11650405-B2

Title: Microscope and method for computational microscopic layer separation

Description:
RELATED APPLICATIONS 
     This application claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Patent Application No. 62/935,791, filed Nov. 15, 2019, and titled “COMPUTATIONAL MICROSCOPIC LAYER SEPARATION,” which is incorporated, in its entirety, by this reference. 
    
    
     BACKGROUND 
     Microscopy is an important field with many applications, such as health care and metrology. Work in relation to the present disclosure suggests that the prior approaches to focusing microscopes on samples and scanning microscope slides can be less than ideal in at least some respects. For example, with some of the prior approaches the amount of time to scan a sample can be longer than would be ideal. Also, automated approaches for setting the focus of the microscope can set the focus incorrectly in at least some instances. 
     In whole-slide digital microscopy, an area in the slide may be scanned by acquiring a series of fields of view (“FOVs”). When preparing a slide, a high refractive index material can be applied on top of the specimen in order to protect it from outside dirt, as well as securing it in place and flattening the sample. These materials may include a glass coverslip, film plastic coverslip, oils, glues or liquid coverslip. The use of a coverslip may result in two layers of data: “legitimate” data in between the slide and the coverslip, and “undesired” data above the coverslip. The latter may include dirt such as dust, glue residues, fingerprints, etc. 
     With prior approaches, dirt on top of the cover slip may be mistaken for legitimate data and may cause auto-focus algorithms to lock onto it in at least some instances. This problem can be more prevalent when the sample scanned is sparse, since in at least some FOVs dirt may be the dominant component in the image. This focusing on an inappropriate layer, such as dirt on top of a slide, can result in degraded microscope data or increased scan times in at least some instances. 
     Another prior approach for distinguishing between the two layers is to perform “z-stack” scanning through the focal planes of a FOV and finding the focal planes of the data along the way, e.g. by using sharpness metrics to determine where features are the sharpest throughout the scan. However, this approach can result in scan times that are longer than would be ideal and datasets that are larger than would be ideal in at least some instances. 
     Another prior approach for identification of the relevant sample layer is by using a special coverslip or slide, where several markings are printed at the interface between the coverslip and the slide. The printed markings could be recognized automatically and help the system reach the correct focal plane. Although helpful for identifying the correct focal plane, this approach relies on additional hardware, as well as algorithms that search for and lock onto the printed markings which may slow down the scan. 
     In light of the forgoing, there is a need for improved systems and methods of focusing microscopes that ameliorate at least some of the aforementioned limitations. Ideally these systems and methods would focus the microscope at an appropriate sample plane, without relying on additional hardware or appreciably increasing the time to scan a sample. 
     SUMMARY 
     In some embodiments, the systems and methods described herein provide improved scanning of microscope samples with improved placement of focal planes for data acquisition within samples, which can decrease scan times and the size of data obtained with a scan of a microscope slide. In some embodiments, one or more optical aberrations is measured and the focal plane adjusted in response to the aberrations. While the aberrations can be measured in many ways, in some embodiments the one or more aberrations is measured by illuminating the sample at a plurality of angles and an amount of the one or more aberrations determined in response to a shift among the plurality of images. The microscope may comprise an imaging device that images the sample through a coverslip with decreased aberrations as compared to material on the coverslip such as dirt. In some embodiments, the processor is configured with instructions to advance a focal plane toward a sample or not to advance the focal plane in response to an amount of the one or more aberrations. 
     In some embodiments, a microscope for computational microscopic layer separation comprises an imaging device that includes a lens and an image sensor, an illumination system for illuminating a sample, and an actuator to adjust an axial position of a focal plane with respect to the sample. The microscope may also include a processor operatively coupled to the imaging device and the illumination system. The processor may be configured to measure, using the image sensor and the illumination system, optical aberrations of the imaging device at the axial position, and determine whether to adjust the focal plane with respect to the sample in response to the one or more optical aberrations. 
     INCORPORATION BY REFERENCE 
     All patents, applications, and publications referred to and identified herein are hereby incorporated by reference in their entirety and shall be considered fully incorporated by reference even though referred to elsewhere in the application. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       A better understanding of the features, advantages and principles of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, and the accompanying drawings of which: 
         FIG.  1    shows a diagram of an exemplary microscope, in accordance with some embodiments; 
         FIGS.  2 A-B  show diagrams of a focal plane of an exemplary microscope, in accordance with some embodiments; 
         FIG.  3    shows a flow chart of a method of computational microscopic layer separation, in accordance with some embodiments; and 
         FIG.  4    shows a flow chart of a process of computational microscopic layer separation, in accordance with some embodiments. 
     
    
    
     DETAILED DESCRIPTION 
     The following detailed description and provides a better understanding of the features and advantages of the inventions described in the present disclosure in accordance with the embodiments disclosed herein. Although the detailed description includes many specific embodiments, these are provided by way of example only and should not be construed as limiting the scope of the inventions disclosed herein. 
     The present disclosure is generally directed to systems and methods for computational microscopic layer separation that may allow for correcting focus errors related to aberrations and to identify the sample for scanning, as compared to other material such as dirt on a coverslip. As will be explained in greater detail below, embodiments of the instant disclosure may be configured to measure one or more optical aberrations of an imaging device at an axial position. The focal plane of the imaging device may be adjusted with respect to the sample in response to the optical aberrations. The systems and methods described herein may improve the field of digital microscopy by being able to adjust the focal plane without the use of specialized hardware or microscope design. 
     The presently disclosed systems and methods are well suited for use with prior microscopes such as computational microscopes, and can be incorporated into and combined with such prior systems. An exemplary microscope suitable for modification in accordance with the present disclosure is described in U.S. Pat. No. 10,705,326, granted on Jul. 7, 2020, entitled “Autofocus system for a computational microscope”, the entire disclosure of which is incorporated herein by reference. 
     Tomography refers generally to methods where a three-dimensional (3D) sample is sliced computationally into several 2D slices. Confocal microscopy refers to methods for blocking out-of-focus light in the image formation which improves resolution and contrast but tends to lead to focusing on a very thin focal plane and small field of view. Although reference is made to computational microscopy, the presently disclosed systems and methods are well suited for use with many types of microscopy such as one or more of a high definition microscope, a digital microscope, a computational microscope, a 3D microscope, a phase imaging microscope, a phase contrast microscope, a dark field microscope, a differential interference contrast microscope, a lightsheet microscope, a confocal microscope, a holographic microscope, or a fluorescence-based microscope 
     The following will provide, with reference to  FIGS.  1 - 4   , detailed descriptions of computational microscopic layer separation.  FIGS.  1  and  2 A -B illustrate a microscope and various microscope configurations.  FIGS.  3  and  4    illustrate an exemplary processes for computational microscopic layer separation. 
       FIG.  1    is a diagrammatic representation of a microscope  100  consistent with the exemplary disclosed embodiments. In some embodiments, the microscope comprises a device or instrument for magnifying an object which is smaller than easily observable by the naked eye, i.e., creating an image of an object for a user where the image is larger than the object. In some embodiments, the microscope comprises an optical microscope that uses light in combination with an optical system for magnifying an object. An optical microscope may be a simple microscope having one or more magnifying lens. In some embodiments, the microscope comprises a computational microscope, which comprises an image sensor and image-processing algorithms to enhance or magnify the object&#39;s size or other properties, such as resolving power of the microscope. The computational microscope may be a dedicated device or created by incorporating software and/or hardware with an existing optical microscope to produce high-resolution digital images. As shown in  FIG.  1   , microscope  100  comprises an image capture device  102 , a focus actuator  104 , a controller  106  connected to memory  108 , an illumination assembly  110 , and a user interface  112 . An example usage of microscope  100  may be capturing images of a sample  114  mounted on a stage  116  located within the field-of-view (FOV) of image capture device  102 , processing the captured images, and presenting on user interface  112  a magnified image of sample  114 . 
     Image capture device  102  may be used to capture images of sample  114 . In some embodiments, the image capture device comprises a device that records the optical signals entering a lens as an image or a sequence of images. The optical signals may be in the near-infrared, infrared, visible, and ultraviolet spectrums. Examples of an image capture device comprise a CCD camera, a CMOS camera, a color camera, a photo sensor array, a video camera, a mobile phone equipped with a camera, a webcam, a preview camera, a microscope objective and detector, etc. Some embodiments may comprise only a single image capture device  102 , while other embodiments may comprise two, three, or even four or more image capture devices  102 . In some embodiments, image capture device  102  may be configured to capture images in a defined field-of-view (FOV). Also, when microscope  100  comprises several image capture devices  102 , image capture devices  102  may have overlap areas in their respective FOVs. Image capture device  102  may have one or more image sensors (not shown in  FIG.  1   ) for capturing image data of sample  114 . In other embodiments, image capture device  102  may be configured to capture images at an image resolution higher than VGA, higher than 1 Megapixel, higher than 2 Megapixels, higher than 5 Megapixels, 10 Megapixels, higher than 12 Megapixels, higher than 15 Megapixels, or higher than 20 Megapixels. In addition, image capture device  102  may also be configured to have a pixel size smaller than 15 micrometers, smaller than 10 micrometers, smaller than 5 micrometers, smaller than 3 micrometers, or smaller than 1.6 micrometer. 
     In some embodiments, microscope  100  comprises focus actuator  104 . In some embodiments, the focus actuator comprises a device capable of converting input signals into physical motion for adjusting the relative distance between sample  114  and image capture device  102 . Various focus actuators may be used, including, for example, linear motors, electrostrictive actuators, electrostatic motors, capacitive motors, voice coil actuators, magnetostrictive actuators, etc. In some embodiments, focus actuator  104  may comprise an analog position feedback sensor and/or a digital position feedback element. Focus actuator  104  is configured to receive instructions from controller  106  in order to make light beams converge to form a clear and sharply defined image of sample  114 . In the example illustrated in  FIG.  1   , focus actuator  104  may be configured to adjust the distance by moving image capture device  102 . 
     However, in other embodiments, focus actuator  104  may be configured to adjust the distance by moving stage  116 , or by moving both image capture device  102  and stage  116 . Microscope  100  may also comprise controller  106  for controlling the operation of microscope  100  according to the disclosed embodiments. Controller  106  may comprise various types of devices for performing logic operations on one or more inputs of image data and other data according to stored or accessible software instructions providing desired functionality. For example, controller  106  may comprise a central processing unit (CPU), support circuits, digital signal processors, integrated circuits, cache memory, or any other types of devices for image processing and analysis such as graphic processing units (GPUs). The CPU may comprise any number of microcontrollers or microprocessors configured to process the imagery from the image sensors. For example, the CPU may comprise any type of single- or multi-core processor, mobile device microcontroller, etc. Various processors may be used, including, for example, processors available from manufacturers such as Intel®, AMD®, etc. and may comprise various architectures (e.g., x86 processor, ARM®, etc.). The support circuits may be any number of circuits generally well known in the art, including cache, power supply, clock and input-output circuits. Controller  106  may be at a remote location, such as a computing device communicatively coupled to microscope  100 . 
     In some embodiments, controller  106  may be associated with memory  108  used for storing software that, when executed by controller  106 , controls the operation of microscope  100 . In addition, memory  108  may also store electronic data associated with operation of microscope  100  such as, for example, captured or generated images of sample  114 . In one instance, memory  108  may be integrated into the controller  106 . In another instance, memory  108  may be separated from the controller  106 . 
     Specifically, memory  108  may refer to multiple structures or computer-readable storage mediums located at controller  106  or at a remote location, such as a cloud server. Memory  108  may comprise any number of random access memories, read only memories, flash memories, disk drives, optical storage, tape storage, removable storage and other types of storage. 
     Microscope  100  may comprise illumination assembly  110 . In some embodiments, the illumination assembly comprises a device or system capable of directing light to illuminate sample  114 , such as illumination at a plurality of angles. 
     Illumination assembly  110  may comprise any number of light sources, such as light emitting diodes (LEDs), LED array, lasers, and lamps configured to emit light, such as a halogen lamp, an incandescent lamp, or a sodium lamp. For example, illumination assembly  110  may comprise a Kohler illumination source. Illumination assembly  110  may be configured to emit polychromatic light. For instance, the polychromatic light may comprise white light. 
     In one embodiment, illumination assembly  110  may comprise only a single light source. Alternatively, illumination assembly  110  may comprise four, sixteen, or even more than a hundred light sources organized in an array or a matrix. In some embodiments, illumination assembly  110  may use one or more light sources located at a surface parallel to illuminate sample  114 . In other embodiments, illumination assembly  110  may use one or more light sources located at a surface perpendicular or at an angle to sample  114 . 
     In addition, illumination assembly  110  may be configured to illuminate sample  114  in a series of different illumination conditions. In one example, illumination assembly  110  may comprise a plurality of light sources arranged in different illumination angles, such as a two-dimensional arrangement of light sources. In this case, the different illumination conditions may comprise different illumination angles. For example,  FIG.  1    depicts a beam  118  projected from a first illumination angle α 1 , and a beam  120  projected from a second illumination angle α 2 . In some embodiments, first illumination angle α 1  and second illumination angle α 2  may have the same value but opposite sign. In other embodiments, first illumination angle α 1  may be separated from second illumination angle α 2 . However, both angles originate from points within the acceptance angle of the optics. In another example, illumination assembly  110  may comprise a plurality of light sources configured to emit light in different wavelengths. In this case, the different illumination conditions may comprise different wavelengths. For instance, each light source may be configured to emit light with a full width half maximum bandwidth of no more than 50 nm so as to emit substantially monochromatic light. In yet another example, illumination assembly  110  may be configured to use a number of light sources at predetermined times. In this case, the different illumination conditions may comprise different illumination patterns. For example, the light sources may be arranged to sequentially illuminate the sample at different angles to provide one or more of digital refocusing, aberration correction, or resolution enhancement. Accordingly and consistent with the present disclosure, the different illumination conditions may be selected from a group including: different durations, different intensities, different positions, different illumination angles, different illumination patterns, different wavelengths, or any combination thereof. 
     Consistent with disclosed embodiments, microscope  100  may comprise, be connected with, or in communication with (e.g., over a network or wirelessly, e.g., via Bluetooth) user interface  112 . In some embodiments, a user interface comprises a device suitable for presenting a magnified image of sample  114  or any device suitable for receiving inputs from one or more users of microscope  100 .  FIG.  1    illustrates two examples of user interface  112 . The first example is a smartphone or a tablet wirelessly communicating with controller  106  over a Bluetooth, cellular connection or a Wi-Fi connection, directly or through a remote server. The second example is a PC display physically connected to controller  106 . In some embodiments, user interface  112  may comprise user output devices, including, for example, a display, tactile device, speaker, etc. In other embodiments, user interface  112  may comprise user input devices, including, for example, a touchscreen, microphone, keyboard, pointer devices, cameras, knobs, buttons, etc. With such input devices, a user may be able to provide information inputs or commands to microscope  100  by typing instructions or information, providing voice commands, selecting menu options on a screen using buttons, pointers, or eye-tracking capabilities, or through any other suitable techniques for communicating information to microscope  100 . User interface  112  may be connected (physically or wirelessly) with one or more processing devices, such as controller  106 , to provide and receive information to or from a user and process that information. In some embodiments, such processing devices may execute instructions for responding to keyboard entries or menu selections, recognizing and interpreting touches and/or gestures made on a touchscreen, recognizing and tracking eye movements, receiving and interpreting voice commands, etc. 
     Microscope  100  may also comprise or be connected to stage  116 . Stage  116  comprises any horizontal rigid surface where sample  114  may be mounted for examination. Stage  116  may comprise a mechanical connector for retaining a slide containing sample  114  in a fixed position. The mechanical connector may use one or more of the following: a mount, an attaching member, a holding arm, a clamp, a clip, an adjustable frame, a locking mechanism, a spring or any combination thereof. In some embodiments, stage  116  may comprise a translucent portion or an opening for allowing light to illuminate sample  114 . For example, light transmitted from illumination assembly  110  may pass through sample  114  and towards image capture device  102 . In some embodiments, stage  116  and/or sample  114  may be moved using motors or manual controls in the XY plane to enable imaging of multiple areas of the sample. 
       FIG.  2 A  illustrates a basic schematic of an exemplary microscope according to some embodiments.  FIG.  2 A  illustrates a microscope  200  (which may correspond to microscope  100 ), that may include a image capture device  202  (which may correspond to image capture device  102 ), a focus actuator  204  (which may correspond to focus actuator  104 ), a controller  206  (which may correspond to controller  106 ) connected to a memory  208  (which may correspond to memory  108 ), an illumination assembly  210  (which may correspond to illumination assembly  110 ), a tube lens  232 , an objective lens  234 , a sample  214  mounted on a stage  216  (which may correspond to stage  116 ), and a lateral actuator  236 . Sample  214  may include a specimen  246  (e.g., the actual sample to be scanned), between a slide  242  and a coverslip  244  (having a thickness  245 ), and potentially dirt  248  on coverslip  244 . Tube lens  232  and objective lens  234  may function in unison to focus light of a focal plane  250  (which may be determined based on a position of objective lens  234  as adjusted by focus actuator  204 ) of sample  214  in an FOV of image capture device  202 . Tube lens  232  may comprise a multi-element lens apparatus in a tube shape, which focuses light in conjunction with objective lens  234 . Lateral actuator  236  may comprise a motor or other actuator described herein that may be capable of physically moving stage  226  laterally in order to adjust a relative lateral position between sample  214  and image capture device  202 . In some examples, focus actuator  204  and/or lateral actuator  236  may comprise a coarse actuator for long range motion and a fine actuator for short range motion. The coarse actuator may remain fixed while the fine focus actuator of focus actuator  204  adjusts the focal distance and lateral actuator  236  moves the lateral position of sample  214  for the movement paths. The coarse actuator may comprise a stepper motor and/or a servo motor, for example. The fine actuator may comprise a piezo electric actuator. The fine actuator may be configured to move sample  214  by a maximum amount within a range from 5 microns to 500 microns. The coarse actuator may be configured to move sample  214  by a maximum amount within a range from 1 mm to 100 mm. 
     Stage  216  may be configured to hold sample  214 . Illumination assembly  210  may comprise an illumination source configured to illuminate sample  214 . Image capture device  202  may be configured to capture multiple images or frames of sample  214  within an FOV of image capture device  202  at focal plane  250 . Lateral actuator  236  may be configured to change a relative lateral position between image capture device  202  and an imaged portion of sample  214  within the FOV of image capture device  202  for each of the multiple images. Focus actuator  204  may be configured to adjust a focal distance (e.g., focal plane  250 ) between sample  214  and image capture device  202  between each of the multiple captured images. Controller  206 , may comprise a processor operatively coupled to lateral actuator  236 , focus actuator  204 , image capture device  202 , and/or illumination assembly  210  in order to move sample  214  laterally relative to the FOV and capture an area of sample  214  one or more times. In some examples, controller  206  may be configured to apply each of multiple light colors (using illumination assembly  210 ) for one or more captures. 
     Although the examples herein describe adjusting the relative lateral position by physically moving stage  216 , in other embodiments the relative lateral position may be adjusted in other ways, including moving/shifting one or more of image capture device  202 , tube lens  232 , objective lens  234 , sample  214 , and/or stage  216 . Likewise, although the examples herein describe adjusting the focal distance by physically moving objective lens  234 , in other embodiments the focal distance may be adjusted in other ways, including moving/shifting one or more of image capture device  202 , tube lens  232 , objective lens  234 , sample  214 , and/or stage  216 . 
     As seen in  FIG.  2 A , focal plane  250  may lie within dirt  248 , which may not be desirable. Dirt  248  may lie on coverslip  244 . Specimen  246 , which may be a sample prepared for imaging, may be protected between coverslip  244  and slide  242 . Coverslip  244  may comprise a solid or liquid coverslip comprising a transparent material such that image capture device  202  may capture specimen  246  through coverslip  244 . However, because coverslip  244  may be transparent, focal plane  250  lying within dirt  248  on top of coverslip  244  may appear as legitimate data (e.g., may be confused for specimen  246 ). In some embodiments, the imaging device is configured to measure the sample with decreased aberrations through the coverslip as opposed to material located on top of the coverslip such as dirt, which can be related to the index of refraction of air as compared to the index of refraction of the coverslip. 
       FIG.  2 B  shows microscope  200 , which may be correctly focused on sample  214  such that focal plane  250  lies within specimen  246 . As will be described further below, microscope  200  may detect that focal plane  250  lies within dirt  248  (in  FIG.  2 A ), and correct, via controlling focus actuator  204  to move objective lens  234 , focal plane  250  by shifting focal plane  250  down into specimen  246 , as seen in  FIG.  2 B . Although the present disclosure describes shifting focal plane  250  down, in other embodiments focal plane  250  may be shifted up and/or down as needed, using focus actuator  204  and/or lateral actuator  236  as needed. 
       FIG.  3    illustrates a flow chart of an exemplary method  300  for computational microscopic layer separation. In one example, each of the steps shown in  FIG.  3    may represent an algorithm whose structure includes and/or is represented by multiple substeps, examples of which will be provided in greater detail below. 
     As illustrated in  FIG.  3   , at step  310  one or more of the systems described herein may measure, using the image sensor and the illumination system, one or more optical aberrations of the imaging device at the axial position. For example, controller  206  may measure, using image capture device  202  and illumination assembly  210 , one or more optical aberrations of microscope  200  at the axial position, which may correspond to focal plane  250 . 
     The optical aberrations may manifest in various ways. In some examples, the optical aberrations may comprise a spherical aberration. In some examples, the optical aberrations may comprise coma and/or astigmatism. In some examples, the optical aberrations may not comprise defocus. In other examples, the optical aberrations may comprise two or more optical aberrations, which may include defocus. 
     In some embodiments, one or more of image shifting, blurring or a spatially varying point spread function may be detected in acquired images in response to different illumination angles of the sample. Some aberrations, such as astigmatism and trefoil, can result in non-uniform image shifting in response to the plurality of illumination angles, which can be used to detect the type and amount of aberration. With astigmatism, the image shifting in response to the plurality of illumination angles may occur greater in one direction than another direction, e.g. asymmetrical, for example. With spherical aberration, such as fourth order and sixth order spherical aberration, the image shifting may remain substantially symmetrical with respect to the change in illumination angle, for example. In some embodiments, the amount of the image shifting for defocus may correspond to the angle of illumination. For example, a first illumination angle α 1  closer to 90 degrees will provide less image shift than a second illumination angle α 2  that is farther from 90 degrees than 90 degrees. 
     In some embodiments, one or more of the types of aberrations or the amount of the one or more aberrations is determined in response to the one or more of image shifting, blurring or a spatially varying point spread function. In some embodiments, the point spread function of the imaging system varies slowly across the image, and the amount of aberrations is determined in response to the spatially varying point spread function. In some embodiments, a portion of the image is analyzed, such that the change in the image related to illumination angle corresponds to one or more of the amount or type of the one or more aberrations. In some embodiments, a plurality of portions is analyzed to determine the localized aberrations for each of the plurality of portions of the image. Alternatively or in combination, each of the plurality of portions can be analyzed to determine change in image structure in response to the plurality of illumination angles. Although reference is made to image shifting to determine one or more of an amount or type of aberrations, in some embodiments the one or more aberrations is determined without measuring image shifting, for example with an artificial intelligence algorithm such as one or more of machine learning, a neural network, or a convolutional neural network and other approaches and combinations thereof as described herein, which can detect subtle change in image structure related to the one or more aberrations in order to determine the one or more aberrations. 
     Optionally, at step  320  one or more of the systems described herein may capture, using the image sensor, image data from a plurality of images at the axial position using the plurality of illumination angles. For example, controller  206  may capture, using image capture device  202 , image data from multiple images at the axial position (e.g., focal plane  250 ), using multiple illumination angles from illumination assembly  210 . 
     In some examples, illumination assembly  210  may be configured to illuminate sample  214  (e.g., specimen  246 ) at a plurality of illumination angles. For instance, illumination assembly  210  may comprise a variable illumination source, such as an LED array positioned to illuminate sample  214  with one or more plane waves or approximate plane waves, from different angles at different times. Illumination assembly  210  may illuminate sample  214  with more than one plane wave at the same time, such as pairs of plane waves from different angles. 
     More specifically, illumination assembly  210  may include a plurality of light sources. In some examples, controller  206  may illuminate the sample from the plurality of illumination angles simultaneously with simultaneous activation of a plurality of light sources using illumination assembly  210 . In other examples, controller  206  may illuminate the sample from the plurality of illumination angles sequentially with sequential activation of the plurality of light using illumination assembly  210 . 
     Optionally, at step  330  one or more of the systems described herein may calculate an amount of shift in the image data between the plurality of images. For example, controller  206  may calculate the amount of shift in the image data between the plurality of images. The shift in the image data and corresponding illumination angles can be used to determine the amount of the one or more aberrations as described herein. 
     In some examples, controller  206  may use one or more of cross-correlation, a feature extraction and matching algorithm, and/or a data driven algorithm such as neural networks to detect an effective shift in each of the images acquired using illumination assembly  210  at different angles of illumination. 
     In some examples, controller  206  may use knowledge of the properties of the optical system, such as numerical aperture (“NA”), and the effective shift calculated above to construct a set of linear and/or non-linear equations. Controller  206  may solve the set of equations to determine the unknown aberrations. 
     In some examples, to reduce a number of unknowns in the set of equations, controller  206  may know or partially know some of the aberrations and/or defocus. For example, sample  214  may be sufficiently defocused in one direction such that a magnitude of the defocus is determined. In other examples, controller  206  may already know one or more of the aberrations. For instance, controller  206  may comprise values corresponding to known amounts of aberrations except for defocus and spherical aberrations in order to achieve a more robust reconstruction via the equations. In another example, controller  206  comprise values corresponding only a magnitude and/or sign of some aberrations. In yet other examples, controller  206  may have values corresponding to the sign of some aberrations such that the constructed equations may be non-linear. 
     In some embodiments, if it is a priori known, e.g. based on the system configuration, that most of the aberrations are insignificant or known, and only some aberrations (e.g., defocus and/or spherical aberrations) are significant, controller  206  may consider only defocus and/or spherical aberrations as unknowns and consider the rest of the aberrations as known or ignored (if unknown) when solving the equations. The measured aberrations (which may or may not include defocus), may be used as the initial condition for computational microscopy reconstruction. 
     Optionally, at step  340  one or more of the systems described herein may determine, using the calculated amount of shift or other image data as described herein, a distance between the sample and the focal plane. For example, controller  206  may determine, using the calculated amount of shift, a distance between focal plane  250  and specimen  246 . 
     In some examples, controller  206  may determine whether an object located at the focal plane is in focus in response to an image shift from images captured with the image sensor and to adjust the axial position of the focal plane in response to the object being in focus and an amount of the one or more aberrations above a threshold amount. As will be explained further below, controller  206  may adjust focal plane  250  in response to dirt  248  being in focus and the amount of aberrations exceeding a threshold amount. In some examples, controller  206  may determine the adjustment based in part on thickness  245  of coverslip  244 , which may be known, in order to adjust focal plane  250  into specimen  246 . 
     Although optional steps  320 - 340  are presented sequentially after step  310  in  FIG.  3   , in some embodiments one or more of steps  320 - 340  may comprise substeps of step  310 . In other embodiments, one or more of steps  320 - 340  may be performed or skipped as appropriate. 
     Optionally, at step  350  one or more of the systems described herein may determine whether the focal plane is located on one or more of on a surface of a transparent material covering the sample, beneath a surface of the transparent material covering the sample or within the sample in response to an amount of the one or more aberrations. For example, controller  206  may determine whether focal plane  250  is located on a surface of coverslip  244 , beneath the surface of coverslip  244 , or within specimen  246 , in response to the amount of aberrations. 
     In some examples, focal plane  250  may comprise an axial location within a depth of field of image capture device  202 . 
     In some examples, image capture device  202  may be configured to image sample  214  with the transparent material (e.g., coverslip  244 ) covering sample  214  with a decreased amount of aberrations as compared to the transparent material not covering sample  214 . Controller  206  may be configured with instructions to adjust focal plane  250  toward sample  214  (e.g., as seen the shift in focal plane  250  from  FIG.  2 A  to  FIG.  2 B ) in order to decrease the one or more aberrations. 
     In some examples, image capture device  202  may be configured to image an object with decreased aberrations with focal plane  250  of image capture device  202  located beneath an upper surface of the transparent covering material (e.g., coverslip  244 ) as compared to focal plane  250  located on or above the upper surface. 
     In some examples, controller  206  may be configured to determine whether focal plane  250  is located on dirt  248  on a surface of the transparent material (e.g., coverslip  244 ) covering sample  214  (e.g., specimen  246 ) or on sample  214  beneath the surface of the covering material in response to the amount of the one or more aberrations and a structure of an image captured with image capture device  202  at the axial position. For example, controller  206  may determine whether focal plane  250  is located on dirt  248 , as in  FIG.  2 A , or on specimen  246 , as in  FIG.  2 B , in response to one or more of the amount of aberrations detected, or a structure of the image captured. 
     In some examples, sample  214  (e.g., specimen  246 ) may comprise a sparse sample. In some examples, the transparent material (e.g. coverslip  244 ) covering sample  214  may comprise a solid coverslip and/or a liquid coverslip. In some examples, the transparent material covering sample  214  may comprise an index of refraction of at least 1.4. 
     In some examples, controller  206  may be configured to determine the amount of the one or more aberrations in response to the calculated amount of shift, as described herein. For example, the amount of the one or more optical aberrations may be compared to a predetermined value of the one or more optical aberrations. Additionally, the axial position may be adjusted in response to the amount being greater than the predetermined value or not adjusted in response to the amount being less than the predetermined value. 
     In some examples, controller  206  may be configured to determine whether the one or more optical aberrations correspond to a presence of a transparent material (e.g., coverslip  244 ) covering sample  214  between the lens (e.g., objective lens  234  and/or tube lens  232 ) and focal plane  250 . 
     Although  FIG.  3    illustrates optional step  350  as sequentially following step  340 , in some embodiments step  350  may comprise a substep of any of the steps of method  300 , such as a substep of step  310 . In some embodiments, one or more of steps  320 - 340  may be performed or skipped before step  350 . In some embodiments, step  350  may be performed before one or more of steps  320 - 340 , in conjunction with one or more of steps  320 - 340 , or alternatively to one or more of steps  320 - 340 . 
     At step  360  one or more of the systems described herein may determine whether to adjust the focal plane with respect to the sample in response to the one or more optical aberrations. For example, controller  206  may determine, based on the one or more optical aberrations, to adjust focal plane  250 , such as the shift depicted between  FIG.  2 A  and  FIG.  2 B  as further described herein. 
     Although  FIG.  3    illustrates a specific sequence of steps, in other embodiments the steps may be performed in another order, simultaneously, skipped, or repeated, such as one or more of optional steps  320 - 350 . 
       FIG.  4    illustrates a flow chart of an exemplary method  400  for computational microscopic layer separation. In one example, each of the steps shown in  FIG.  4    may represent an algorithm whose structure includes and/or is represented by multiple substeps, examples of which will be provided in greater detail below. 
     As illustrated in  FIG.  4   , at step  410  one or more of the systems described herein may begin with a new FOV. For example, controller  206  may adjust objective lens  234  and/or stage  216 , using focus actuator  204  and/or lateral actuator  236 , to initial or default positions after sample  214  is mounted onto stage  216  to start scanning. Although focal plane  250  should preferably be located at specimen  246 , as in  FIG.  2 B , focal plane  250  may possibly be in an undesired position, as in  FIG.  2 A . In one example, controller  206  may have erroneously autofocused onto dirt  248 , or otherwise incorrectly adjusted focal plane  250 . 
     At step  420  one or more of the systems described herein may detect data in one layer (e.g., one focal plane). For example, controller  206 , using image capture device  202 , may capture data using a current position of focal plane  250 . Depending on where focal plane  250  is positioned, the data captured may be legitimate (e.g., in  FIG.  2 B ), or may be unwanted data (e.g., in  FIG.  2 A ). 
     At step  430  one or more of the systems described herein may determine if the detected data is legitimate or dirt. For example, controller  206  may determine whether the detected data is legitimate (e.g., focal plane  250  is located within specimen  246  as in  FIG.  2 B ) or dirt (e.g., focal plane  250  is located within dirt  248  as in  FIG.  2 A ). Controller  206  may determine whether the detected data is legitimate by, for example as described above, detecting a number of aberrations and comparing the number of detected aberrations to a threshold value of aberrations. If the detected number exceeds the threshold value, the detected data may be dirt, and method  400  may proceed to step  450 . Otherwise, the detected data may be legitimate, and method  400  may proceed to step  440 . 
     If the detected data is determined to be legitimate, then at step  440  one or more of the systems described herein may stay in place, if the detected data is legitimate data. For example, controller  206  may not shift focal plane  250  as focal plane  250  may already be located within specimen  246 , as in  FIG.  2 B . 
     If the detected data is determined to be dirt, then at step  450  one or more of the systems described herein may move down the coverslip, if the detected data is dirt. For example, controller  206  may determine how much axial adjustment is needed to move focal plane  250  beyond coverslip  244  and into specimen  246 , as described above. Controller  206  may accordingly control focus actuator  204  to move objective lens  234  and/or lateral actuator  236  to move stage  216  such that focal plane  250  is moved from dirt  248 , as seen in  FIG.  2 A , into specimen  246 , as seen in  FIG.  2 B . 
     At step  460  one or more of the systems described herein may continue scanning. For example, once focal plane  250  is at a desired position within specimen  246 , controller  206  may control image capture device  202  to captured image data of specimen  246  and continue the scanning of sample  214 . 
     The steps of method  400  may be performed in any order and repeated as needed. For example, multiple focal planes of specimen  246  may be scanned, and one or more of the desired focal planes may undergo method  400 . 
     As described herein, the computing devices and systems described and/or illustrated herein broadly represent any type or form of computing device or system capable of executing computer-readable instructions, such as those contained within the modules described herein. In their most basic configuration, these computing device(s) may each comprise at least one memory device and at least one physical processor. 
     The term “memory” or “memory device,” as used herein, generally represents any type or form of volatile or non-volatile storage device or medium capable of storing data and/or computer-readable instructions. In one example, a memory device may store, load, and/or maintain one or more of the modules described herein. Examples of memory devices comprise, without limitation, Random Access Memory (RAM), Read Only Memory (ROM), flash memory, Hard Disk Drives (HDDs), Solid-State Drives (SSDs), optical disk drives, caches, variations or combinations of one or more of the same, or any other suitable storage memory. 
     In addition, the term “controller”, “processor” or “physical processor,” as used herein, generally refers to any type or form of hardware-implemented processing unit capable of interpreting and/or executing computer-readable instructions. In one example, a physical processor may access and/or modify one or more modules stored in the above-described memory device. Examples of physical processors comprise, without limitation, microprocessors, microcontrollers, Central Processing Units (CPUs), Field-Programmable Gate Arrays (FPGAs) that implement softcore processors, Application-Specific Integrated Circuits (ASICs), portions of one or more of the same, variations or combinations of one or more of the same, or any other suitable physical processor. The processor may comprise a distributed processor system, e.g. running parallel processors, or a remote processor such as a server, and combinations thereof. 
     Although illustrated as separate elements, the method steps described and/or illustrated herein may represent portions of a single application. In addition, in some embodiments one or more of these steps may represent or correspond to one or more software applications or programs that, when executed by a computing device, may cause the computing device to perform one or more tasks, such as the method step. 
     In addition, one or more of the devices described herein may transform data, physical devices, and/or representations of physical devices from one form to another. Additionally or alternatively, one or more of the modules recited herein may transform a processor, volatile memory, non-volatile memory, and/or any other portion of a physical computing device from one form of computing device to another form of computing device by executing on the computing device, storing data on the computing device, and/or otherwise interacting with the computing device. 
     The term “computer-readable medium,” as used herein, generally refers to any form of device, carrier, or medium capable of storing or carrying computer-readable instructions. Examples of computer-readable media comprise, without limitation, transmission-type media, such as carrier waves, and non-transitory-type media, such as magnetic-storage media (e.g., hard disk drives, tape drives, and floppy disks), optical-storage media (e.g., Compact Disks (CDs), Digital Video Disks (DVDs), and BLU-RAY disks), electronic-storage media (e.g., solid-state drives and flash media), and other distribution systems. 
     A person of ordinary skill in the art will recognize that any process or method disclosed herein can be modified in many ways. The process parameters and sequence of the steps described and/or illustrated herein are given by way of example only and can be varied as desired. For example, while the steps illustrated and/or described herein may be shown or discussed in a particular order, these steps do not necessarily need to be performed in the order illustrated or discussed. 
     The various exemplary methods described and/or illustrated herein may also omit one or more of the steps described or illustrated herein or comprise additional steps in addition to those disclosed. Further, a step of any method as disclosed herein can be combined with any one or more steps of any other method as disclosed herein. 
     The processor as described herein can be configured to perform one or more steps of any method disclosed herein. Alternatively or in combination, the processor can be configured to combine one or more steps of one or more methods as disclosed herein. 
     Unless otherwise noted, the terms “connected to” and “coupled to” (and their derivatives), as used in the specification and claims, are to be construed as permitting both direct and indirect (i.e., via other elements or components) connection. In addition, the terms “a” or “an,” as used in the specification and claims, are to be construed as meaning “at least one of” Finally, for ease of use, the terms “including” and “having” (and their derivatives), as used in the specification and claims, are interchangeable with and shall have the same meaning as the word “comprising. 
     The processor as disclosed herein can be configured with instructions to perform any one or more steps of any method as disclosed herein. 
     It will be understood that although the terms “first,” “second,” “third”, etc. may be used herein to describe various layers, elements, components, regions or sections without referring to any particular order or sequence of events. These terms are merely used to distinguish one layer, element, component, region or section from another layer, element, component, region or section. A first layer, element, component, region or section as described herein could be referred to as a second layer, element, component, region or section without departing from the teachings of the present disclosure. 
     As used herein, the term “or” is used inclusively to refer items in the alternative and in combination. 
     As used herein, characters such as numerals refer to like elements. 
     The present disclosure includes the following numbered clauses. 
     Clause 1. A microscope comprising: at least one imaging device comprising lens and an image sensor; an illumination system for illuminating a sample; an actuator to adjust an axial position of a focal plane with respect to the sample; and a processor operatively coupled to the at least one imaging device and the illumination system, the processor configured to: measure, using the image sensor and the illumination system, one or more optical aberrations of the imaging device at the axial position; and determine whether to adjust the focal plane with respect to the sample in response to the one or more optical aberrations. 
     Clause 2. The microscope of clause 1, wherein the processor is configured to determine whether the focal plane is located on one or more of on a surface of a transparent material covering the sample, beneath a surface of the transparent material covering the sample or within the sample in response to an amount of the one or more aberrations. 
     Clause 3. The microscope of clause 2, wherein the imaging device is configured to image the sample with the transparent material covering the sample with a decreased amount of aberrations as compared to the transparent material not covering the sample and wherein the processor is configured with instructions to adjust the focal plane toward the sample in order to decrease the one or more aberrations. 
     Clause 4. The microscope of clause 2, wherein the imaging device is configured to image an object with decreased aberrations with the focal plane of the imaging device located beneath an upper surface of the transparent material as compared to the focal plane located on or above the upper surface. 
     Clause 5. The microscope of clause 2, wherein the processor is configured to determine whether the focal plane is located on dirt on a surface of the transparent material covering the sample or on the sample beneath the surface of the transparent material in response to the amount of the one or more aberrations and a structure of an image captured with the at least one imaging device at the axial position. 
     Clause 6. The microscope of clause 5, wherein the sample comprises a sparse sample. 
     Clause 7. The microscope of clause 2, wherein the transparent material covering the sample comprises one or more of a solid coverslip or a liquid coverslip. 
     Clause 8. The microscope of clause 2, wherein the transparent material covering the sample comprises an index of refraction of at least 1.4. 
     Clause 9. The microscope of clause 1, further comprising an illumination system to illuminate a sample at a plurality of illumination angles. 
     Clause 10. The microscope of clause 9, wherein the processor is configured to: capture, using the image sensor, image data from a plurality of images at the axial position using the plurality of illumination angles; calculate an amount of shift in the image data between the plurality of images; and determine, using the calculated amount of shift, a distance between the sample and the focal plane. 
     Clause 11. The microscope of clause 10, wherein the processor is configured to determine the amount of the one or more aberrations in response to the calculated amount of shift. 
     Clause 12. The microscope of clause 10, wherein the processor is configured to illuminate the sample from the plurality of illumination angles simultaneously with simultaneous activation of a plurality of light sources. 
     Clause 13. The microscope of clause 12, wherein the processor is configured to illuminate the sample from the plurality of illumination angles sequentially with sequential activation of the plurality of light sources. 
     Clause 14. The microscope of clause 1, wherein the amount of the one or more optical aberrations is compared to a predetermined value of the one or more optical aberrations and optionally wherein the axial position is adjusted in response to the amount being greater than the predetermined value or not adjusted in response to the amount being less than the predetermined value. 
     Clause 15. The microscope of clause 1, wherein the processor is configured to determine whether the one or more optical aberrations correspond to a presence of a transparent material covering the sample between the lens and the focal plane. 
     Clause 16. The microscope of clause 1, wherein the processor is configured with instructions to determine whether an object located at the focal plane is in focus in response to an image shift from images captured with the image sensor and to adjust the axial position of the focal plane in response to the object being in focus and an amount of the one or more aberrations above a threshold amount. 
     Clause 17. The microscope of clause 1, wherein the one or more optical aberrations comprises a spherical aberration. 
     Clause 18. The microscope of clause 17, wherein the one or more optical aberrations comprises one or more of coma or astigmatism. 
     Clause 19. The microscope of clause 1, wherein the one or more optical aberrations does not comprise defocus. 
     Clause 20. The microscope of clause 1, wherein the one or more optical aberrations comprise two or more optical aberrations and wherein the two or more optical aberrations include defocus. 
     Clause 21. The microscope of clause 1, wherein the focal plane comprises an axial location within a depth of field of the at least one imaging device. 
     Clause 22. A method comprising: illuminating a sample with an illumination system; imaging the sample with at least one imaging device comprising lens and an image sensor; adjusting, with an actuator, an axial position of a focal plane with respect to the sample; and measuring, using the image sensor and the illumination system, one or more optical aberrations of the imaging device at the axial position; and determining whether to adjust the focal plane with respect to the sample in response to the one or more optical aberrations. 
     Embodiments of the present disclosure have been shown and described as set forth herein and are provided by way of example only. One of ordinary skill in the art will recognize numerous adaptations, changes, variations and substitutions without departing from the scope of the present disclosure. Several alternatives and combinations of the embodiments disclosed herein may be utilized without departing from the scope of the present disclosure and the inventions disclosed herein. Therefore, the scope of the presently disclosed inventions shall be defined solely by the scope of the appended claims and the equivalents thereof