Abstract:
A system for extracting material from a region of interest includes a fluid delivery base comprising an inlet channel and an outlet channel formed within the fluid delivery base; a gasket affixed to the fluid delivery base, wherein the gasket comprises at least one opening exposing an open end of the inlet channel and an open end of the outlet channel; a support comprising a sample-supporting surface facing the gasket and an opposing surface; and an alignment member coupled to the opposing surface in a fixed position and such that the support is positioned between the fluid delivery base and the alignment member, wherein one or both of the alignment member or the fluid delivery base are biased towards one another by a force (e.g., a magnet or spring force) and wherein the fluid delivery base is separable from the support and configured to move along a plane of the sample-supporting surface to align with the alignment member.

Description:
BACKGROUND 
     The subject matter disclosed herein relates to techniques for extracting biological molecules from an existing sample, such as a pathology slide. 
     Medical researchers often obtain patient samples, such as biopsies, and preserve such samples as pathology slides, core samples, etc., for diagnosis and visualization. When such samples contain particular regions of interest, the researchers may wish to extract materials from these regions of interest for additional studies. For example, researchers may examine a slide including both tumor and normal cells, and may wish to extract DNA from only the tumor cells in the slide to assess the DNA for the presence of particular mutations. However, extraction of material from only a region of interest and without damaging the material is complex. For example, in laser capture micro-dissection, a focused laser beam ablates tissue to define a region of interest but damage the surrounding material. Other techniques may involve tissue encapsulation, which introduces an additional material to the sample. 
     BRIEF DESCRIPTION 
     Certain embodiments commensurate in scope with the originally claimed invention are summarized below. These embodiments are not intended to limit the scope of the claimed invention, but rather these embodiments are intended only to provide a brief summary of possible forms of the invention. Indeed, the invention may encompass a variety of forms that may be similar to or different from the embodiments set forth below. 
     In one embodiment, a system for extracting material from a region of interest includes a fluid delivery base. The system also includes a first channel within the fluid delivery base and terminating at a first channel end at a sample-facing surface of the fluid delivery base, wherein the first channel comprises a first channel opening configured to couple to a fluid inlet to fluidically couple the fluid inlet the first channel end and a second channel within the fluid delivery base and terminating at a second channel end at the sample-facing surface of the fluid delivery base, wherein the second channel comprises a second channel opening configured to couple to fluid outlet to fluidically couple the fluid outlet to the second channel end. The system also includes a gasket coupled to the sample-facing surface and comprising a gasket opening aligned with an area of the sample-facing surface comprising the first channel end and the second channel end. The system also includes a support comprising a sample-supporting surface facing the gasket and an opposing surface and an alignment member coupled to the opposing surface, wherein the fluid delivery base is separable from the support and configured to move along a plane of the sample-supporting surface to align with the alignment member. 
     In another embodiment, a method of extracting material from a region of interest includes the steps of aligning one or more fluid channels of a fluid delivery base with an alignment member to define a region of interest on a sample, wherein the fluid delivery base and the alignment member are positioned on opposing surfaces of the sample such that the fluid delivery base and the alignment member are separated from one another by at least the sample and wherein the aligning comprises changing a position of the fluid delivery base or the alignment member relative to one another; delivering extraction fluid to the sample via the one or more fluid channels; and collecting the extraction fluid via the one or more fluid channels. 
     In yet another embodiment, a system for extracting material from a region of interest includes a fluid delivery base comprising one or more channels formed within the fluid delivery base, wherein the fluid delivery base comprises a metal; a gasket affixed to the fluid delivery base, wherein the gasket comprises at least one opening exposing an open end of at least one of the one or more channels; a support comprising a sample-supporting surface facing the gasket and an opposing surface; and an alignment member coupled to the opposing surface in a fixed position and such that the support is positioned between the fluid delivery base and the alignment member, wherein the fluid delivery base is separable from the support and configured to move along a plane of the sample-supporting surface to align with the alignment member. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       These and other features, aspects, and advantages of the present invention will become better understood when the following detailed description is read with reference to the accompanying drawings in which like characters represent like parts throughout the drawings, wherein: 
         FIG. 1  is a partial cross-sectional view of an extraction system in accordance with embodiments of the present techniques; 
         FIG. 2  is a partial cross-sectional view of the extraction system of  FIG. 1  showing the isolation area on the sample; 
         FIG. 3  is a top view of an exemplary extraction system showing multiple regions of interest on the sample; 
         FIG. 4  is a schematic view of a magnetic field of a magnetic fluid delivery base and a magnetic alignment member in accordance with embodiments of the present techniques; 
         FIG. 5  is a cross-sectional view of a fluid delivery base in accordance with embodiments of the present techniques; 
         FIG. 6  is a perspective view of an extraction system in contact with a sample in accordance with embodiments of the present techniques; 
         FIG. 7  is a perspective view of an alternative extraction system in contact with a sample in accordance with embodiments of the present techniques; 
         FIG. 8  is a partial cross-sectional view of an extraction system including an internal light in accordance with embodiments of the present techniques; 
         FIG. 9  is a schematic representation of a technique for aligning the separable fluid delivery base of an extraction system with a fixed alignment member in accordance with embodiments of the present techniques; 
         FIG. 10  is a schematic representation of a technique for aligning the separable fluid delivery base of an extraction system with a removable alignment member in accordance with embodiments of the present techniques; 
         FIG. 11  is a side view of an extraction system including an adjustable arm in accordance with embodiments of the present techniques; 
         FIG. 12  a partial cross-sectional view of a multi-region of interest extraction system in accordance with embodiments of the present techniques; 
         FIG. 13  is a schematic representation of a technique for aligning the fluid delivery base of a fluid extraction device with a sample on an x-y-z stage in accordance with embodiments of the present techniques; 
         FIG. 14  is a stained image of a colon adenocarcinoma with the top panel showing DNA staining and including background, the middle panel showing staining with the background removed and the bottom panel after region of extraction removal; and 
         FIG. 15  is stained image of a breast invasive ductal carcinoma with the top panel showing DNA staining and including background, the middle panel showing staining with the background removed and the bottom panel after region of extraction removal. 
     
    
    
     DETAILED DESCRIPTION 
     Researchers may wish to extract regions of interest from biological or environmental samples with minimal disruption of the original slide or section. A region of interest may be any user-defined region on a sample, and may be a single cell, a subcellular region, or a multicellular region of a sample. Regardless of the region of interest for the user, techniques used for extracting regions of interest from the sample may damage the surrounding sample and/or may be expensive or complex. For example, laser-based techniques may be used that cut around a particular region of interest, but such techniques may involve expensive equipment, skilled technicians, and long processing times. For example, laser capture microdissection may involve complex associated sample preparation and is performed by skilled technicians Other techniques target a region of interest via transfer, such as applying liquid wax on a slide and removing the wax after solidification. However, such techniques are difficult to automate and provide only limited spatial resolution, in certain cases because the wax is difficult to limit to a particular location with high resolution. In another example, extraction may be achieved by physically scraping (and wasting) away all of the non-ROI tissue. Such physical extractions are associated with a destruction of the remaining sample, which prevents further analysis or sample mapping. 
     Provided herein is a self-aligning region of interest extraction technique that provides improved spatial resolution without complex equipment. In addition, the present techniques provide high extraction efficiencies for materials of interest within the sample, such as nucleic acids, without damaging the surrounding tissue. In turn, surrounding sample preservation allows for more complex analysis to be performed on a sample, such as mapping or heterogeneity analysis. The present techniques are also suitable for automation or higher throughput. 
     The disclosed techniques may be used in conjunction with samples of biological materials. As used herein, the term “biological material” refers to material obtained from samples of a biological subject, including biological tissue or fluid obtained from a subject. Such samples may be, but are not limited to, body fluid (e.g., blood, blood plasma, serum, or urine), tissues, fractions, and cells isolated from, or located in, any biological system, such as mammals. Biological samples and/or biological materials also may include sections of the biological sample including tissues (e.g., sectional portions of an organ or tissue). Biological samples may also include extracts from a biological sample, for example, a population of cells from a biological fluid (e.g., blood or urine). In certain embodiments, the biological material may include proteins, nucleic acids, carbohydrates, fatty acids, and/or small molecules. It should be understood that the samples may be histological samples, pathology samples, or tissue core samples and may be in the form of slides, sections, multi-well plates, etc. Further, the disclosed techniques may also be used in conjunction with non-biological samples, environmental samples, or forensic samples. 
     Turning to  FIG. 1 , the extraction system  10  as provided herein includes a fluid delivery base  12  that, in operation, is positioned to deliver extraction fluid directly to the sample  14 . The sample  12  is positioned on a top surface  16  of a support  20 . A bottom surface  22  of the support  20  opposes the top surface and is coupled to or includes an alignment member  24 . In operation, the fluid delivery base  12  is applied to the sample  14  by operator or machine manipulation. In one embodiment, the alignment member  24  and the fluid delivery base  12  self-align under magnetic force to hold the fluid delivery base  12  in position on the sample  14 . In certain embodiments, one or both of the fluid delivery base  12  or the alignment member  24  is a magnet, e.g., a permanent magnet or an electromagnet. Such that the fluid delivery base  12  and the alignment member  24  magnetically align to hold the fluid delivery base  12  in place. 
     When the fluid delivery base  12  is aligned or correctly positioned on the sample  14 , a gasket  30  on a sample-facing surface  32  of the fluid delivery base  12  comes into direct contact with the sample. Once a portion of the sample is isolated via the gasket  30 , fluid delivery for extraction may take place. As depicted, the fluid delivery base  12  may include a fluid inlet channel  34  for delivering an extraction fluid, represented by arrow  36 , to the isolated sample portion. Further, the fluid delivery base may include a fluid outlet channel  38  for collecting the incubated extraction liquid and recovered materials e.g., biological materials, represented by arrow  40 . 
     The fluid delivery base  12  may include the channels  34  and  38  as integrally formed passageways within the body of the fluid delivery base  12 . For example, the channels  34  and  38  may be formed via drilling or as part of an injection mold die. While the depicted embodiment includes a single inlet channel  34  and outlet channel  38 , it should be understood that there may be any suitable number of channels  34  and  38 , and that the channels  34  and  38  may be present in equal or unequal numbers. Further, the size (e.g., inner diameter) of each channel  34  or  38  may be selected based on a desired region of interest size. That is, for relatively small regions of interest, the channels  34  and  38  may be formed with correspondingly small inner diameters. In certain embodiments, the inlet and outlet functions may be achieved via a single channel used for inflow and outflow. Further, while the channels  34  and  38  may be formed within the fluid delivery base, in other embodiments, the fluid delivery base  12  may form a central passage (e.g. may be donut-shaped) that facilitates insertion of preformed channels  34  and  38  within the passageway. Such an embodiment may help keep the fluid delivery base  12  isolated from contact with biological materials, which may in turn facilitate reuse. 
     The inlet channel  34  terminates at channel end  44  and the outlet channel  38  terminates at channel end  46  on the sample-facing surface  32  and within an area  48  defined by the gasket  30 . In the depicted embodiment, the channels  34  and  38  are substantially parallel to one another and open at respective channel ends  50  and  52  disposed on a top surface  54  of the fluid delivery base  12 . However, in other embodiments, the channels  34  and  38  may open on a side surface  58  and/or open at a specialized junction to accommodate couplings to upstream or downstream tubing. Further, the inlet and outlets channels  34  and  38  may be angled or nonparallel depending on the desired configuration of the fluid delivery base  12 . 
     The fluid delivery base  12 , in certain embodiments, is held in place on the sample  14  via magnetic force.  FIG. 2  is a partial cross-sectional view of the system  10  showing a region of interest that may be isolated by the fluid delivery base  12 . In operation, the gasket  30  makes direct contact with the sample material  60  at a contact area  62  to isolate a region of interest  64 . When the gasket  30  makes direct contact, the extraction fluid from the inlet channel  34  is sealed from lateral diffusion across the sample material  60 , which facilitates targeted extraction and recovery of the extracted material via outlet channel  38 . Further, because the force on the sample  14  is a combination of the gasket sealing force and the magnetic pull force, the applied force may be selected to minimize pressure of the gasket on the sample material  60 . To that end, the gasket may be formed from a relatively compliant sealing material, such as a compressible polymer. In particular embodiments, the gasket  30  may be hydrophobic to discourage any lateral diffusion of extraction fluid. 
     The fluid delivery base  12  and, in particular, the channels  34  and  38  may be configured based on a desired spatial resolution of the region of interest  64 . In certain embodiments, the region of interest  64  may be less than or larger than 1 mm 2  or may be on the order of 100 microns or less. In other embodiments, the region of interest  64  may several centimeters square. Further, the region of interest may have any desired shape, including a circle, square, etc. The gasket  30  may be cut to an opening that defines the desired region of interest size and shape. In one embodiment, the gasket  30  may be cut to an opening that is defined by the system  10 . For example, the system  10  may include imaging software under processor control. The user may view the sample  14  via a user interface and may define the region of interest  64  by providing inputs on the user interface, which may be viewed as a superimposed region on the sample image. Further, the gasket  30  may be selected based on the region of interest  64  or may be custom cut. 
       FIG. 3  is an example of a sample  14  showing region of interests that may be isolated by the fluid delivery base as provided herein. In certain embodiments, the system  10  provides for regions of interest  64  that encompass an edge or border of the sample material  60 . For example, a clinician may wish to determine if cells on a border region have different characteristics than cells in the interior of the sample. The fluid delivery base is capable of isolating and sealing cells within the region of interest  64  even if the region of interest includes an edge, which provides advantages over other techniques that may not be able to isolate edge material. Further, the disclosed techniques may be used with poor quality samples that were either prepared poorly and/or that have degraded. 
       FIG. 4  is a schematic diagram of an embodiment in which both the fluid delivery base  12  and the alignment member  24  are magnets with a magnetic field (e.g., magnetic fields  70  and  72 ). For example, the fluid delivery base  12  is a bar magnet with a south pole  80  oriented towards the region of interest. The alignment member  24  may be oriented so that its north pole  82  is closest to the south pole  80  of the field delivery base  12  so that the fluid delivery base  12  and the alignment member  24  will attract one another as they are positioned closer together (by movement of one or both of the fluid delivery base  12  or the alignment member  24 ) to hold the fluid delivery base  12  on the region of interest  64 . As shown, the alignment may occur along an axis  86  through the alignment member  24 , the region of interest  64 , and the fluid delivery base  12 . Generally, the magnetic field  70  may extend beyond the region of interest  64  and towards the alignment member  24  when the fluid delivery base  12 , via the gasket  30 , is in direct contact with the sample  14 . In addition, in such a configuration, the magnetic field of the alignment member  24  may extend beyond the region of interest  64  and towards the fluid delivery base  12 . 
     It is contemplated that, in embodiments of the present techniques, both the fluid delivery base  12  and the alignment member  24  are magnets. However, in other embodiments, only one of the fluid delivery base  12  or the alignment member  24  is a magnet while the other is formed of or includes a ferrous material. Further, the fluid delivery base  12  or the alignment member  24  may be a permanent magnet, including iron, nickel, cobalt, a rare earth metal magnet, lodestone, a magnetic composite formed from a metallic magnetic material and a ceramic material or resin, a nanomagnet, etc. The fluid delivery base  12  or the alignment member  24  may also include an electromagnet. 
       FIG. 5  illustrates a cross-section of an implementation of a fluid delivery base  12  that may include a non-metallic or non-magnetic portion  90  and a metallic portion  92 . In a particular embodiment, the metallic portion  92  may be magnetic. In the depicted embodiment, the metallic portion  92  is positioned towards the sample end of the fluid delivery base  12 , (i.e., in contact with the gasket  30 ), but in other embodiments, the metallic portion  92  may form an exterior cylinder or casing for the fluid delivery base  12  while the core portion, including the fluid channels, may be formed of a non-metallic or non-ferrous material. 
     The configuration of the fluid delivery base  12  and the alignment member  24  (see  FIG. 2 ) may be selected to achieve sufficient pull force to hold the fluid delivery base  12  without applying so much pressure as to damage the underlying sample when in operation. The magnet pull force may be influenced by the materials of the fluid delivery base  12  and the alignment member  24  (i.e., the magnet strength of certain materials is higher than other materials), and the size of the magnetic material. For example, the height (represented by d 1 ) and width (represented by d 2 ) as well as the depth of the fluid delivery base  12  or the alignment member  24  may influence the pull force. In one embodiment, the pull force, case 1, of the fluid delivery base, is less than 1 lb., e.g., between about 0.32 lb-0.8 lb. However, it should be understood that the pull force is related to the size of the magnet, and larger magnets may have larger pull forces. In one embodiment, a ring magnet having an inner diameter of about 0.06 inches and an outer diameter of about 0.2 inches and a height dimension of about 0.2 inches has a pull force, case 1, of about 0.32 lbs, a pull force, case 2, of about 0.38 lbs, and a pull force, case 3, of about 0.63 lbs may be used. A ring magnet having an inner diameter of about 0.125 inches and an outer diameter of about 0.25 inches and a height dimension of about 0.25 inches has a pull force, case 1, of about 0.64 lbs, a pull force, case 2, of about 0.80 lbs, and a pull force, case 3, of about 1.13 lbs may be used. In another embodiment, the pull force, case 1, is such that an operator may easily manually manipulate the fluid delivery base  12  relative to the sample  14  during removal or application. In the disclosed embodiments, the case 1 pull force is the pull force to remove a magnet from a steel plate, the case 2 pull force is the pull force to remove a first steel plate from a magnet with a second steel plate on an opposing face, and case 3 is the pull force to remove one magnet from another magnet. 
     In the depicted embodiment, the fluid delivery base  12  may include a mix of materials to form a shape that is sufficiently-sized to be gripped by an operator but is not so magnetically strong as to damage the underlying sample. That is, by mixing in materials that are relatively lightweight and nonmetallic, the fluid delivery base  12  may be made larger without being too heavy or without too strong of a magnetic field. 
       FIG. 6  is an example of an implementation of the system  10 , including the fluid delivery base  12  in place on a sample  14 . The fluid delivery base is coupled to inflow tubing  100  and outflow tubing  102  via an adaptor  106 . The adaptor  106  may include interior channels that couple to the inlet and outlet channels  34  and  38  within the fluid delivery base and exterior channels  110  and  112  to couple to the inflow tubing  100  and outflow tubing  102 . It is contemplated that all or part of the portion of the system  10  above the sample  14  (e.g., in contact with the sample  14 ) may be disposable. For example, in one embodiment, the gasket  30  may be removable from the fluid delivery base  12 , which may be cleaned and retained for additional uses while the gasket  30  is discarded. In addition, the adaptor  106  and the tubing  100  and  102  may be provided as a disposable attachment to the fluid delivery base. Alternatively, the fluid delivery base  12  may be assembled as a unitary assembly with the gasket  30  and the adaptor  106  fixed in place on (e.g. bonded or adhered to) the fluid delivery base  12 . In another embodiment, the tubing may couple directly to the fluid delivery base  12  without an adaptor  106  or fluid reservoir. Accordingly, in one embodiment, a sample extraction kit may include a fluid delivery base  12  with a gasket  30  and an adaptor  106  in place on the fluid delivery base  12 . The kit may, in certain embodiments, also include sections of tubing that may be attached, whether during assembly or by an end user, to the exterior channels  110  and  112  to form inflow tubing  100  and outflow tubing  102 . 
     Further, in particular embodiments, such a kit may also include one or more materials for performing an extraction from a sample  14 . For example, if the sample is a paraffin-embedded tissue section on a glass slide, the kit may include proteinase K for nucleic acid extraction. In one embodiment, an adaptor may be packed with a suitable amount of proteinase K to apply to the sample  14  via the fluid delivery base  12 . The kit may also include a selection of gaskets  30  with different opening sizes that facilitate extraction of different-sized regions of interest. An operator may select a gasket  30  with an opening corresponding to the desired region of interest size and apply the gasket  30  prior to the extraction. The gaskets  30  may be removable/replaceable, and may be peeled away and discarded after use. 
       FIG. 7  is an example of an implementation of the fluid delivery base  12  in place on a sample  14  in which a single channel is used for the outlet channels within the fluid delivery base. A coupler including the outlet  114  is fluidically coupled to tubing  116 . The sample may be loaded into an integral reservoir in the fluid delivery base  12 . In operation, the user loads the buffer into the reservoir, which is then pulled to the sample  14 . In addition, the sample  14  is shown with sample material  60  having already been isolated from a region of interest  64  (shown as having the sample material removed in a complete circle) and in place on a second region of interest. 
     In the various embodiments of the system disclosed herein, the isolation and extraction of material from a particular region of interest  64  may be performed in conjunction with enzyme or chemical delivery to the region of interest  64 , e.g., via inlet channel  34  or the coupler  114  to facilitate liquefication of the sample material  60  and subsequent extraction. By performing the extraction on a region of limited size, the extraction workflow may be improved. For example, depending on the enzyme delivered to the region of interest and the temperature of the sample  14 , the incubation time may be on the order of seconds (e.g., less than 10 seconds) rather than several minutes as in other techniques. In particular, more rapid extraction times may be achieved by agitating the fluid including a buffer and enzyme. Increased temperature may also reduce extraction times. However, longer incubation times are also contemplated. Any suitable extraction enzyme may be used, such as proteinase K. In other embodiments, the fluid delivery base  12  may be used for liquefication and extraction that is not chemically or enzymatically mediated. 
       FIG. 8  illustrates a cross-section of an implementation of a fluid delivery base  12  that may include a light source. In operation, as the base  12  moves towards the sample, the emitted light from the light source may help identify the region of interest  64  to assist in proper placement of the fluid delivery base  12  and subsequent material extraction from the sample. For example, the fluid delivery base  12  may include one or more dedicated light channels  120  coupled to a light source  122  (e.g., an LED), which may be on or in the fluid delivery base  12  or may be external to the base  12 . Optical fibers may be disposed in the one or more light channels  120 , or the channel  120  itself may form a light pipe. Such an arrangement may be advantageous because the relatively small footprint of an optical fiber or light pipe may help the spatial resolution of the region of interest  64 , e.g., for regions of interest that are less than 1 mm 2 . However, in cases where the region of interest is larger, the light source may be directly disposed on or in the sample-contacting surface  32  (see  FIG. 1 ) fluid delivery base  12 . 
     The fluid delivery base  12  as provided herein may be used in conjunction with a fixed or separable alignment member  24 .  FIG. 9  is a schematic flow diagram of a technique  200  for using the system  10  with the alignment member  24  fixed in place on (e.g., integral with, adhered to, or part of) the support  20 . For example, in certain embodiments, it may be more convenient and provide more uniform results to have the alignment member  24  fixed in place on the support  20  or sample platform. At step  202 , the operator positions the sample  14  on the support  20  at a sample placement location such that the region of interest  64  corresponds with a location of the alignment member  24  on the opposing surface  22 . In such embodiments, the support  20  may include an indicator or marking that indicates the sample placement location. At step  204 , the fluid delivery base  12  is applied to sample  14  to isolate the region of interest  64  and the alignment member  24  and the fluid delivery base  12  self-align (e.g., the alignment is supported by the strength of the magnetic attraction between these components). Once aligned, the extraction liquid may be introduced at step  206  for incubation and collection of materials extracted from the region of interest. 
       FIG. 10  is a schematic flow diagram of an alternate technique  210  for using the system  10  with a movable alignment member  24 . At step  212 , the operator positions the sample  14  on the support  20 . At step  214 , the operator either positions the alignment member  24  on the opposing surface  22  or, alternatively, activates an alignment member that is fixed in place. In one embodiment, the system  10  may include multiple alignment members  24  but may only activate (e.g., apply current to activate an electromagnet) one of the set. Accordingly, the sample placement location would correspond to the active alignment member. Such an embodiment may permit relatively small alignment members  24  to be used to improve spatial resolution. Once aligned at step  216 , the extraction liquid may be introduced at step  218  for incubation and collection of materials extracted from the region of interest. 
     While the fluid delivery base  12  and/or the alignment member  24  may be positioned manually, the system  10  may also be used in conjunction with a mechanical manipulator. For example,  FIG. 11  is a side view of an extraction device  256  that includes a mechanical arm  250  and coupled to a base holder  252  that holds the fluid delivery base  12 . The base holder  252  changes position relative to the mechanical arm  250  (either by moving or by staying in place when the mechanical arm  250  is moved) to position the fluid delivery base  12  in close proximity to and on the sample  14 . Further, while certain embodiments, of the disclosed techniques relate to magnetic alignment of the fluid delivery base on the sample, the fluid delivery base  12  may also be held in place with other biasing forces, e.g., spring force. 
     The extraction device  256  may also be coupled to a controller  260  that facilitates image analysis of the sample (e.g., sample  14 ) and movement/alignment of the fluid delivery base at a selected region of interest. Accordingly, the extraction device  256  may include an imager  264  that detects signals and converts the signals to data that may be processed by downstream processors. The imager  264  may operate in accordance with various physical principles for creating the image data and may include a fluorescent microscope, a bright field microscope, or devices adapted for suitable imaging modalities. In general, however, the imager  264  creates image data indicative of the sample  14   
     The imager  264  and/or the extraction device  256  and mechanical arm  250  operate under the control of system control circuitry  262 . The system control circuitry  262  may include a wide range of circuits, such as illumination source control circuits, timing circuits, circuits for coordinating data acquisition in conjunction with sample movements, circuits for controlling the position of light sources and detectors and the fluid delivery base  12 , and so forth. In the present context, the system control circuitry  262  may also include computer-readable memory elements, such as magnetic, electronic, or optical storage media, for storing programs and routines executed by the system control circuitry  262  or by associated components of the system  10 . The stored programs or routines may include programs or routines for performing all or part of the present technique. 
     Image data acquired by the imager  256  may be processed by the imager  12 , for a variety of purposes, for example to convert the acquired data or signal to digital values, and provided to data acquisition circuitry  266 . The data acquisition circuitry  266  may perform a wide range of processing functions, such as adjustment of digital dynamic ranges, smoothing or sharpening of data, as well as compiling of data streams and files, where desired. The data acquisition circuitry  266  may also transfer acquired image data to data processing circuitry  270  where additional processing and analysis may be performed. The controller  260  may include one or more processor-based components, such as general purpose or application-specific computers. In addition to the processor-based components, the computer may include various memory and/or storage components including magnetic and optical mass storage devices and/or internal memory, such as RAM chips. The memory and/or storage components may be used for storing programs and routines for performing the techniques described herein that are executed by the operator workstation or by associated components of the system  10 . Alternatively, the programs and routines may be stored on a computer accessible storage medium and/or memory remote from the operator workstation but accessible by network and/or communication interfaces present on the computer. In one embodiment, the controller  260  may facilitate operator selection of a region of interest  64  (e.g., via a user interface) on an image of the sample  14  acquired by the image  264  and displayed via the user interface. The controller  260  may also control movement of the fluid delivery base  12  via the mechanical arm  250  to position the fluid delivery base  12  on the region of interest  64 . The controller  260  may also control fluid inflow and outflow, and may include one or more settings for controlling flow rate and/or incubation time. 
     The extraction techniques disclosed herein may also be used in parallel, as shown in  FIG. 12 , which illustrates a fluid delivery base  12  capable of isolating multiple regions of interest  64  in parallel. Such a configuration may be used for sample mapping, and the system  10  may extract biological materials from multiple locations on a sample slide for further analysis. Accordingly, in certain embodiments, the controller  260  ( FIG. 11 ) may be used to define multiple regions of interest. Alternatively, the positioning may occur manually.  FIG. 13  is a schematic view of a technique  300  for manipulating the fluid delivery base  12  relative to the sample  14  using the fluid extraction device  256 . The operator views selects or view automatically selected regions of interest superimposed on an acquired image on a workstation  302 , which may be coupled to the controller  260  (see  FIG. 11 ). The operator may provide inputs to select or confirm the regions of interest, which activates movement of a stage holding the sample  14 , the fluid delivery base  12 , or both as indicated by arrow  310  to correctly align the fluid delivery base  12  on the region/s of interest. The stage may be an x-y-z stage with freedom of movement in the x, y, and z directions. Further, the fluid delivery base  12  may also include an actuator or stage in the x, y, and/or z direction. In the case of multiple regions of interest  64 , the fluid delivery base may be positioned concurrently on all of them (with associated separate isolation gaskets  30 ), or may be operated to align with each in series. Fluid extraction, represented by arrow  312 , occurs once the fluid delivery base  12  is positioned in place. The alignment may occur via an imaging or registration step in which the coordinates of the region of interest  64  are acquired during imaging and the fluid extraction device is controlled to position the fluid delivery base  12  at the appropriate coordinates. 
     Selection of the regions of interest  64  may be coupled to the image acquisition. For example, the sample  14  may be stained with one or more stains specific for biological markers. The regions of interest  64  may include the regions that are positive for the biological markers. The controller  260  may be configured to align the fluid delivery base  12  with the areas of the sample  14  positive for biological markers of interest. In this manner, biomolecules, cells, and/or regions expressing specific proteins or markers may be extracted from the sample  14  for further analysis. In one embodiment, an operator may select the biomarker of interest via the workstation  302  and the controller  260  may automatically extract regions including the biomarker. 
     The following is an example of an extraction performed with an extraction system, such as the systems disclosed herein. For region of interest extractions on colon tissue, the extraction diameter was 2 mm. Table 1 shows the extraction results: 
     
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 Extraction of Colon Tissue 
               
             
          
           
               
                   
                 Sample 1 
                 Sample 2 
                 Sample 3 
                 Sample 4 
               
               
                   
                   
               
             
          
           
               
                 DNA (ng/uL) 
                 6.70 
                 6.82 
                 7.70 
                 9.13 
               
               
                 Total DNA Yield (ng) 
                 36.83 
                 34.08 
                 42.37 
                 43.83 
               
               
                 DNA (ng)/mm{circumflex over ( )}2) 
                 11.73 
                 10.86 
                 13.49 
                 13.96 
               
               
                   
               
             
          
         
       
     
     The following is an example of an extraction performed with an extraction system, such as the systems disclosed herein.  FIG. 14  shows images before and after extraction. Table 2 shows the extraction results: 
     
       
         
               
             
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 Extraction of Colon Adenocarcinoma 
               
             
          
           
               
                   
                 Sample 1 
                 Sample 2 
               
               
                   
                   
               
             
          
           
               
                   
                 DNA (ng/uL) (w/background) 
                 8.03 
                 10.57 
               
               
                   
                 DNA (ng/uL) (w/o background) 
                 7.30 
                 9.75 
               
               
                   
                 Extraction Volume 
                 5.6 
                 5.2 
               
               
                   
                 Total DNA Yield (ng) 
                 40.91 
                 50.74 
               
               
                   
                   
               
             
          
         
       
     
     The following is an example of an extraction performed with an extraction system, such as the systems disclosed herein.  FIG. 15  shows images before and after extraction. Table 3 shows the extraction results: 
     
       
         
               
             
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 3 
               
             
             
               
                   
               
               
                 Extraction of Breast Invasive Ductal Carcinoma. 
               
             
          
           
               
                   
                 Sample 1 
                 Sample 2 
               
               
                   
                   
               
             
          
           
               
                   
                 DNA (ng/uL) (w/background) 
                 9.71 
                 15.76 
               
               
                   
                 DNA (ng/uL) (w/o background) 
                 8.65 
                 14.27 
               
               
                   
                 Extraction Volume 
                 5.4 
                 5.2 
               
               
                   
                 Total DNA Yield (ng) 
                 46.71 
                 74.23 
               
               
                   
                   
               
             
          
         
       
     
     Technical effects of the invention include rapid isolation of regions of interest in a biological material without introducing a foreign material to the remainder of the sample and without wasting or damaging the remainder. The fluid delivery base as disclosed is configured to isolate a region of interest for extraction by self-aligning with other components of the system. Further, the extraction system provided herein provides isolation of the sample to prevent sample and/or caregiver contamination. By providing a platform for sealing a region of interest, liquefying the isolated contents of the region of interest, and recovering the liquefied material, the sample recovery is faster and more efficient relative to other techniques. In addition, the region of interest is isolated from other areas of the sample, preserving the remaining sample for further study. 
     This written description uses examples to disclose the invention, including the best mode, and also to enable any person skilled in the art to practice the invention, including making and using any devices or systems and performing any incorporated methods. The patentable scope of the invention is defined by the claims, and may include other examples that occur to those skilled in the art. Such other examples are intended to be within the scope of the claims if they have structural elements that do not differ from the literal language of the claims, or if they include equivalent structural elements with insubstantial differences from the literal languages of the claims.