EP4673751A1

EP4673751A1 - Apparatus and methods for baking tissue slides in a slide basket

Info

Publication number: EP4673751A1
Application number: EP24764362.0A
Authority: EP
Inventors: Flemming Lassen NIELSEN; Lene KOFOED
Original assignee: Agilent Technologies Inc
Current assignee: Agilent Technologies Inc
Priority date: 2023-03-02
Filing date: 2024-02-20
Publication date: 2026-01-07
Also published as: WO2024182165A1; AU2024230567A1

Abstract

Specimens in an embedding medium are attached to slides by heating (e.g., baking). Slides with the tissue sections or other embedded specimens are inserted in a slide basket which holds them vertically. The slide basket is placed into a heating chamber which has a sorbent support.

Description

APPARATUS AND METHODS FOR BAKING TISSUE SLIDES IN A SLIDE BASKET

RELATED APPLICATIONS

[0001] This application claims priority to and benefit of U.S. Patent Application No. 63/487,908, filed on March 2, 2023, the content of which is incorporated herein by reference in its entirety.

TECHNICAL FIELD

[0002] The present invention generally relates to preparation of embedded specimens such as tissue section for analysis and/or storage. More particularly, the present invention relates to baking or other heating of embedded specimens so that they adhere to slides.

BACKGROUND

[0003] In histology, pathology and related fields, a biological specimen such as cellular tissue is collected from a human or animal and then subjected to various processing steps in preparation for being examined by an analytical instrument such as a light microscope or electron microscope. A typical preparative process may include fixing, processing (dehydration and stiffener infiltration), embedding, sectioning, drying, and staining.

[0004] Biological specimens are frequently embedded in paraffin or another embedding medium to facilitate handling and so that they might be stored for a potentially long period of time. In an embedding procedure, specimens can be placed in cassettes containing the specimens are brought to an embedding station. The embedding station includes a hot melt gun containing melted paraffin and a chill plate. The technician opens one cassette and selects a mold that will comfortably fit the tissue inside the tissue cassette. The technician places a small amount of paraffin in the base of the mold, and then arranges the tissue in the mold as the paraffin solidifies on the chill plate. The technician then fills the rest of the mold with melted paraffin. Next, the technician places the backside of the tissue cassette against the paraffin and may add a further amount of paraffin. This produces an embedded sample, often referred to as a tissue block. The tissue cassette carries barcode information and acts at a holder for the tissue block. The technician then sets the mold aside until the paraffin hardens, and then removes the tissue block from the mold. The resulting tissue block is often referred to as formalin fixed paraffin embedded (FFPE) tissue.

[0005] Microtomes are used to section (cut) the tissue block to obtain one or more thin slices of the embedded sample. Usually the thickness of these tissue slices is on the order of 4 to 6 micrometers (pm), although a range of 1 micrometer to 30 micrometers is not uncommon. In many staining protocols, the goal is to get a cross-section of the tissue that is approximately one cell thick. The technician cuts several sections, which tend to form a ribbon. The ribbon is carefully placed in a heated water bath to flatten both the paraffin and the tissue or other specimen. The technician then singulates the ribbon into individual tissue sections and draws up one or more tissue sections onto a slide. At this point, each slide consists of one, two, or several sections of tissue and embedding medium held onto the slide by surface tension from a very thin film of water. [0006] For most staining or analytical protocols, the tissue sections need to be carefully dried on the slide, as it is critical that the sections fully adhere to the slides. Drying often entails airdrying the slides for about twenty minutes in a vertical orientation to allow the water to flow to the bottom of the section and then evaporate. This process puts the tissue into direct contact with the glass microscope slide. After drying, the slides are often baked at about 60 °C. Usually the slide is placed flat on a hot plate or in a heated chamber (e.g., an oven) for about twenty minutes to an hour. The length of the drying and baking time varies depending on the subsequent staining process to be performed. For instance, the baking protocol tends to be longer for slides that will be stained for immunohistochemistry (IHC) than for the standard H&E staining because IHC is a more aggressive chemistry and hence increases the likelihood of tissue sections falling off the slides.

[0007] There are some variants to the heating apparatus available, but they generally involve the use of heated chambers or hot plates in some form. This process of drying and baking is done to ensure adhesion of the tissue to the slide throughout the staining process and potentially a decade or more of subsequent storage. A specimen that separates from the slide is usually unusable or lost, the consequence of which can be serious such as in the case of a patient who experienced surgery to obtain the tissue sample.

[0008] As mentioned, slide baking is usually done to ensure adhesion of the specimen on the surface of the slide. Slide baking is characterized by local habits and individual preferences, but overall, it is characterized by significant manual handling. Other ways to handle the process include wooden blocks with cutouts, aluminum foil trays, and flat baking plates. The above examples are intended to address the risk that paraffin melts and subsequently stiffens touching both slide and basket, which might leave the slides stuck in the basket. After baking, the slides are again reloaded into the slide basket for further processing. This process demands a considerable handling time, and additionally adds significant risks of handling errors, such as sorting errors and positioning errors.

[0009] There remains a need for more efficient techniques of slide baking so that specimen such as tissue sections adhere to slides.

SUMMARY

[0010] To address the foregoing problems, in whole or in part, and/or other problems that may have been observed by persons skilled in the art, the present disclosure provides methods, processes, systems, apparatus, instruments, and/or devices, as described by way of example in implementations set forth below.

[0011] According to one aspect, a method is provided for baking a plurality of slides having embedded specimens on the slides. The method comprises inserting one or more slides into a slide basket configured to hold a plurality of the slides. Each of the inserted slides has an embedded specimen on a surface of the slide, and the slide basket has one or more basket supports configured to contact a slide edge of the slides while defining a basket opening that exposes the slide edge. The method also comprises positioning the slide basket on a slide baking device comprising a sorbent support so that the sorbent support contacts the exposed slide edge of one or more of the slides and separates the exposed slide edges from the basket supports. The method also comprises heating the slides having the embedded specimens while in the slide basket and while the slide edges are separated from the one or more basket supports, thereby reducing or preventing flow of melted embedding medium onto the slide basket.

[0012] According to another aspect, a slide baking device is provided for baking a plurality of slides having embedded specimens on the slides. The slide baking device comprises a baking tray comprising a tray base, and a sorbent support. The tray base is configured to hold the sorbent support.

[0013] According to another aspect, a slide baking apparatus is provided, comprising a slide baking device as described herein and a heating chamber comprising a heating element to supply heat to an interior volume of the chamber. The interior volume of the chamber is a size sufficient to receive the baking tray and one or more slide baskets positioned on the baking tray.

[0014] According to another aspect, a method is provided for reducing contamination of a slide basket with melted embedding medium. The slide basket comprises at least one slide having a tissue section embedded in said embedding medium thereon. The method comprises placing a bottom surface of at least one slide in contact with a sorbent member under conditions where the embedding medium melts and flows toward the bottom surface of the slide. The melted embedding medium is sorbed by the sorbent member.

[0015] According to another aspect, a slide baking tray comprises a base having at least one sorbent member thereon. The slide baking tray is configured to receive melted embedded medium from a slide when said slide baking tray is placed adjacent to a slide holding device comprising said slide.

[0016] Other devices, apparatuses, methods, features and advantages of the invention will be or will become apparent to one with skill in the art upon examination of the following figures and detailed description. It is intended that all such additional devices, apparatuses, systems, methods, features, and advantages be included within this description, be within the scope of the invention, and be protected by the accompanying claims.

BRIEF DESCRIPTION OF THE DRAWINGS

[0017] The present invention can be better understood by referring to the following figures. The components in the figures are not necessarily to scale, emphasis instead being placed upon illustrating the principles of the invention. In the figures, like reference numerals designate corresponding parts throughout the different views.

[0018] FIG. l is a perspective view of a slide with an embedded specimen on its surface.

[0019] FIG. 2 is a perspective view of an example of a slide basket according to an embodiment of the present disclosure. [0020] FIG. 3 is a schematic perspective view of an example of a slide baking apparatus according to an embodiment of the present disclosure.

[0021] FIGs. 4A and 4B are schematic views of a slide baking apparatus, illustrating an example of its operation according to an embodiment of the present disclosure.

DEFINED TERMINOLOGY

[0022] It is to be understood that the terminology used herein is for purposes of describing particular embodiments only and is not intended to be limiting. The defined terms are in addition to the technical and scientific meanings of the defined terms as commonly understood and accepted in the technical field of the present teachings.

[0023] As used herein, the terms "substantial" or "substantially" mean to within acceptable limits or degree to one having ordinary skill in the art. For example, "substantially cancelled" means that one skilled in the art considers the cancellation to be acceptable.

[0024] As used herein, the terms "approximately" and "about" mean to within an acceptable limit or amount to one having ordinary skill in the art. The term "about" generally refers to plus or minus 15% of the indicated number. For example, "about 10" may indicate a range of 8.5 to 11.5. For example, "approximately the same" means that one of ordinary skill in the art considers the items being compared to be the same.

[0025] As used herein, the terms "a," "an," and "the" include both singular and plural referents, unless the context clearly dictates otherwise. Thus, for example, "a recess" includes one recess and plural recesses. The terms “first” and “second” are terms to distinguish different elements, not terms supplying a numerical limit, and a device having first and second element can also include a third, a fourth, a fifth, and so on, unless otherwise indicated. [0026] As disclosed herein, various numbers, values and ranges are provided. It should be understood that each range constitutes a disclosure of each intervening value between the upper and lower limits of that range, to the tenth of the unit of the lower limit. It should be understood that smaller ranges are also disclosed, such as a range defined by any stated value or intervening value in a stated range.

[0027] The term “slide” as used herein refers to any solid surface on which an embedded specimen can be placed. Slides are generally relatively thin structures comprising a substantially flat surface, and can be made of glass, plastic, paper, membranes (e.g. nitrocellulose) or fabrics. Microscope slides are usually transparent or translucent, in order to facilitate optical analysis of a specimen disposed on a surface of the slide. For example a tissue section is usually applied on a glass slide, and optionally covered with a translucent or transparent coverslip, in order to facilitate analysis or viewing of the tissue section using a microscope or other optical instrument.

[0028] The terms “specimen” and “biological specimen” include, but are not limited to, tissue sections, tissue blocks, cells, cell layers, tissue arrays, cellular tissue, decellularized tissue, extracellular matrix (ECM), whole mounts, frozen sections, cell preps, cell suspensions, cytospins, touch preparations or preps, thin preparations or preps, and other biological materials or molecules including blood, urine, cerebrospinal fluids, pleural fluids, ascites fluids, biopsy materials, fine needle aspirates, pap smears, swabbed cells or tissues. Specimens can be collected from a human or animal, or they can be collected from other sources, such as specimens comprising bacteria, viruses, parasites, fungi, yeasts or protozoa. The term specimen and biological specimen are generally interchangeable in the present disclosure. As used herein, the term “tissue section” refers to a piece of tissue that has been obtained from a subject, fixed, sectioned, and mounted on a planar surface, e.g., a microscope slide. [0029] An “embedding medium” is any composition that is substantially solid at room temperature and can be used for embedding or otherwise supporting biological samples for histological or other analyses, such as immunohistochemistry (IHC), in situ hybridization (ISH), special stains, and classical dye stains. An "embedded specimen" is a biological specimen that is partially or completely surrounded and/or infiltrated by an embedding medium, such as a paraffin or an epoxy resin.

[0030] As used herein, the term “formalin-fixed paraffin embedded (FFPE) tissue section” refers to a piece of tissue, e g., a biopsy that has been obtained from a subject, fixed in formaldehyde (e.g., 3%-5% formaldehyde in phosphate buffered saline) or other fixative, embedded in paraffin, cut into thin sections, and then mounted on a planar surface, for example a microscope slide.

[0031] As used in this disclosure, the term “deparaffmization” encompasses deliberate removal of paraffin or other embedding medium. Deparaffmization, prior to staining, is usually required to allow access to targets for antibodies or probes in a subsequent staining process. Solvents used for deparaffmization are, for example, xylene, xylene substitutes and toluene.

[0032] As used herein, the term “sorbent” includes absorbent, adsorbent, or any combination or equivalent thereof. A sorbent material is one which sorbs, i.e., absorbs, adsorbs, or otherwise takes up, another substance(s). Sorption can refer to adsorption and/or absorption. Adsorption is often described as attachment of atoms or molecules from a gas, liquid or dissolved solid to a surface. Absorption is often described as atoms or molecules entering a bulk phase of a liquid or solid material. Generally absorption refers to being taken up by the volume of a material, while adsorption refers to being attached to a surface of a material. [0033] It will be understood that the term “in signal communication” as used herein means that two or more systems, devices, components, modules, or sub-modules are capable of communicating with each other via signals that travel over some type of signal path. The signals may be communication, power, data, or energy signals, which may communicate information, power, or energy from a first system, device, component, module, or sub-module to a second system, device, component, module, or sub-module along a signal path between the first and second system, device, component, module, or sub-module. The signal paths may include physical, electrical, magnetic, electromagnetic, electrochemical, optical, wired, or wireless connections. The signal paths may also include additional systems, devices, components, modules, or sub-modules between the first and second system, device, component, module, or sub-module. [0001] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present teachings, some exemplary methods and materials are now described.

[0002] All patents and publications referred to herein are expressly incorporated by reference.

DETAILED DESCRIPTION

[0034] The present disclosure provides methods and apparatus for baking an embedded specimen (e.g., a paraffin-embedded tissue section) on a slide. Various embodiments of the present methods and apparatus can provide one or more of the following advantages. The present methods and apparatus prevent the slide basket from being contaminated with embedding medium that melts during baking or reduce the amount of contamination, by supporting the slides on a sorbent support so that the slide edges are separated from the slide basket, or by placing a bottom surface of the slide in contact with a sorbent member. This facilitates making the slides freely movable in the slide basket after the baking procedure. Additionally, residual embedding medium can be easily collected by the sorbent support or member, and thereby prevents or reduces contamination of the slide basket. In some embodiments, the sorbent support or member can be removable from the slide baking apparatus, so that it can be easily exchanged when needed or at selected intervals. Furthermore, the present apparatus and methods can facilitate automated handling of slides in the slide basket as the slides can move freely rather than being attached to the slide basket by residual embedding medium.

[0035] The present apparatus and methods can simplify the workflow and reduce errors in a pathology lab and in preparation of slides having embedded specimens on a slide surface. The present apparatus and methods can bypass several manual handling processes and significantly reduces risks of handling errors. Handling time may be reduced because slides need not be removed from the slide basket during drying and baking. Also, the risk of wrongly-positioned slides is minimized because slides should only be placed in the basket once. Residual embedding medium is easily collected by the sorbent support or member and can easily be discarded after the baking procedure. The slide basket can be used as input container for automated slide handling without further handling.

[0036] FIG. 1 is an illustration of a exemplary slide 102 suitable for use in the present methods and apparatus. Though slide 102 can have any desired shape or dimensions, in most laboratories and most instruments, slides 102 typically have a rectangular shape, with two slide surfaces 102a, two short slide edges 102b, and two long slide edges 102c. Slides 102 typically have characteristic lengths L, width W and thickness T. For purposes of description, FIG. 1 includes an illustrative L- W-T coordinate system in relation to slide 102. Exemplary slides include slides having a length Ls of 75 millimeters, a width Ws of 26 millimeters wide (e.g., 3 inches long by 1 inch wide) and a thickness Ts of one millimeter, although the slides may have any dimensions consistent with their intended use.

[0037] Slide 102 has a sample region 103 and a slide information region 104, though in other embodiments, the slides may have more than two regions or only one region. The slide 102 has a label 105 in slide information region 104 which can have a barcode and other information to facilitate identification of the slide by a technician or an automated system. In the sample region 103, the slide 102 has an embedded specimen 106 which comprises a biological specimen 108 in an embedding medium 107. The embedded specimen 106 has been mounted on slide surface 102a. A plurality of slides 102 having embedded specimens 106 can be loaded into a slide basket (as shown in FIG. 2) in a manual or automated process.

[0038] The biological specimen 108 may be subjected to various processing steps after it is acquired initially. For example, where the biological specimen 108 is a tissue from a tissue source, it may be subjected to processing steps such as fixing, dehydration, alcohol removal, paraffin infiltration/embedding, sectioning, or others. In general, providing the embedded specimen 106 includes positioning (placing or mounting) the embedded specimen 106 on a slide 102, such as by placing a tissue section in a water bath and drawing it onto the slide 102.

[0039] In the present disclosure, paraffin is frequently used as an example of an embedding medium 107. Paraffin is frequently used as an embedding medium in the preparation of biological specimens, for sectioning in a microtome to produce tissue sections for histological examination. Nonetheless it is contemplated that other embedding media can be substituted for paraffin in the descriptions of the present methods and apparatus. Other examples of the embedding medium 107 include, but are not limited to, waxes of various types, paramat, paraplats, peel away paraffin, tissue freezing medium, cryonic gel, optimal cutting temperature (OCT) compound, polyester wax, and mixtures thereof. Wax is solid at room temperature; usually consists of a complex mixture of higher hydrocarbons often including esters of higher fatty acids and higher glycols; may be mineral, natural or synthetic in origin; is harder and more brittle than fats; is soluble in oils and fats, and can optionally contain additives that enhance its sample-embedding properties. Paraffin is an example of a mineral wax most commonly used in the histochemical field. Paraffin is a hydrophobic substance typically prepared by distillation of petroleum, and is a mixture of primarily solid saturated hydrocarbons. The paraffin (wax) generally consists of higher polyolefins and often comprises polymers or dimethyl sulfoxide (“DMSO”) is added.

[0040] In some embodiments, the embedding medium is an epoxy resin. In some embodiments, the epoxy resin is a glycidyl epoxy resin. In some embodiments, the epoxy resin is a non-glycidyl epoxy resin. In some embodiments, the epoxy resin is a non-glycidyl resin selected from an aliphatic and cyclo-aliphatic resin. In some embodiments, the epoxy resin is a glycidyl epoxy selected from glycidyl amine, glycidyl ester, glycidyl ether, and a combination thereof. In some embodiments, the epoxy resin is ethylene glycol diglycidyl ether. In some embodiments, the epoxy resin is Araldite, Quetol, Epon 812, Embed 812, Poly-Bed 812, or a combination thereof. In some embodiments, the epoxy resin is a glycerol -based aliphatic epoxy resin. In some embodiments, embedding a tissue in an epoxy resin provides tissue sections having improved morphology.

[0041] FIG. 2 shows an example of a slide basket 210 configured to hold a plurality of slides 202. In this representative embodiment, slide basket 210 is a 20-slide basket. The slide basket 210 can have a slide basket handle 211 integral with the slide basket 210, or the slide basket handle 211 or can lock on and off the slide basket 210. The slide basket handle 211 facilitates automated transport of the slide basket 210 from one station to another station. The slide basket handle 211 can be engaged by a robotic arm that moves the slide basket. In this embodiment, slide basket 210 includes opposing endwalls 213, 214 and opposing sidewalls 215, 216. Basket endwalls 213, 214 and basket sidewalls 215, 216 can be solid or can be formed by partial walls or frames, such as sidewall frames 215a, 215b, 215c. Slide basket 210 also includes basket support 220 to which basket endwalls 213, 214 are connected. Opposing endwalls 213, 214 and sidewalls 215, 216 and basket support 220 collectively define an interior volume of the slide basket 210 into which slides 102 may be positioned vertically lengthwise therein (a standing position). Basket support 220 comprises shelves 226 which support slides 202 and define a basket opening 221 through which slide edges 202b are exposed. Basket opening 221 exposes short slide edges 202b, but in some embodiments, the basket opening is configured to expose long slide edges, or to expose both short slide edges and long slide edges. Basket opening 221 has a width Wi that is less than the slide width Ws. The spacing between sidewall 215 and sidewall 216 is sufficient to accommodate the width of a slide 202 therein (for example, 25 mm (one inch)) with little excess space. In FIG. 2, sidewalls 215, 216 comprise top sidewall frames 215a, 216a middle sidewall frames 215b, 216b, and bottom sidewall frames 215c, 216c, though it is contemplated that a basket sidewall can comprise only top and bottom sidewall frames, or more than one middle sidewall frames.

[0042] In some embodiments, sidewalls 215, 216, or one or more or all of sidewall frames 215a-216c have features configured to hold a slide in the slide basket. In FIG. 2, the slides 202 are held in a vertical orientation in the slide basket 210. More particularly, the slides 202 are held such that the axis of its length LS is vertical oriented. In some embodiments, such features hold the slide in the basket such that the slide is maintained in a desired orientation (e.g., where slide surfaces are substantially vertical) and/or the slide does not contact adjacent slides in the basket, but such features do not restrain the slide from being inserted or removed from the slide basket. As an example of features configured to hold a slide, slide basket 210 in FIG. 2 has a pattern of a protrusions along their length (z-dimension) which define slots between them. Protrusions and slots are aligned on each side of slide basket. In other embodiments, the features comprise a series of recesses in the sidewalls or in one or more or all of sidewall frames. Slots or recesses for holding the slides can have a dimension substantially the same size as slide thickness Ts or, in some embodiments, within 0.1 mm, 0.25 mm, 0.5 mm, 0.75 mm, or 1 mm of Ts. FIG. 2 shows basket 210 including slot 222b and protrusion 223b in sidewall frame 215b. Similar slots and protrusions are disposed in sidewall frames 215a, 215c as well, and aligned protrusions and slots are also present (but not visible in FIG. 2) on sidewall frames 216a, 216b, 216c. Basket support 220 of the slide basket 210 includes opposing support shelves 226 along a length dimension (z-dimension) with each shelf 226 having a size sufficient to support the slide while defining an basket opening 221 (e.g., up to a few millimeters), on which a slide can contact when the slide is positioned in slide basket 210. Each shelf 226 also includes slots 227 and protrusions 228 aligned with protrusions and slots in sidewall frames 215a-216c. Protrusions 228 can project upward into the interior volume of slide basket 210. Protrusions 223 may serve to keep the plurality of slides 202 contained in the slide basket 210 separated at a basket support 220 of slide basket 210. In some embodiments, shelf 226 comprises teeth (shown in FIGs. 4A and 4B) on a side opposite an interior volume of slide basket 210 and protrusions 228. As described below, exterior teeth can be used to interact with a track to move slide basket 210 into and out of various devices.

[0043] In some embodiments, a solvent is applied to the slides 102/202 before or after baking. For example, the slides 202 in the slide basket 210 can be immersed in a solvent tank. A solvent can be applied to the slides 102/202 for one or more purposes, such as removal of some or all of the embedding medium 107, or to remove a solvent from the specimen 108, or to apply a new solvent to the specimen 108. In some embodiments, the slides 202 are immersed in a solvent before and/or after the embedded specimens 106 are subjected to baking. In some embodiments, the solvent tank comprises a prewet solvent suitable as a mounting medium. After a desired period, the slide basket is removed from the solvent tank and moved to a slide baking device or station.

[0044] In some embodiments, a cover (such as a cover slip or cover glass) is placed on the slides 102/202 before or after baking.

[0045] FIG. 3 is a schematic perspective view of a slide baking device 330 for baking slides 302 while held in a slide basket 310. The slide baking device 330 can also be referred to as a slide heating apparatus or a slide baking apparatus. The slide baking device 330 is configured for heating so that the embedded specimen will adhere to the slide, which may be done in preparation for storage, removal of embedding medium, staining, applying one or more solvents or reagents, or for other desired processing or analysis.

[0046] In FIG. 3, the slide baking device 330 is a tray comprising a tray base 332 and tray brackets 334 to facilitate lifting and transporting the baking tray 330. A slide basket 310 loaded with a plurality of slides 302 is being placed on a slide baking tray 330. The slides 302 in the slide basket 310 have embedded specimens on the slide surfaces, which are vertically oriented in this embodiment. The slide basket 310 has one or more basket supports configured to contact a slide edge of the slides 302 while defining a basket opening that exposes the slide edge. The slide basket 310 is positioned over the slide baking device 330, more particularly by positioning the basket opening of the slide basket 310 over the sorbent support 336. The slide basket 310 can be lowered so that the sorbent support contacts the exposed slide edge of the slides 302 and separates the exposed slide edges from the basket supports of slide basket 310 (as shown in FIGs. 4A and 4B). [0047] The slide baking tray 330 can comprise one or more tray brackets 334 extending from the tray base 332, such as two tray brackets extending in a substantially perpendicular direction from the tray base 332. The tray brackets 334 can be engaged by a user or by a robotic arm in order to move the slide baking tray 330 from a loading location to a heating location.

[0048] In some embodiments, the slide baking tray 330 comprises a heating element, such as a heating element which is in or on the tray base 332. In some embodiments, the slide baking tray 330 is placed in an oven in order to bake the slides 302. In such embodiments, the slide baking device comprises the slide baking tray 330 and a heating chamber such as an oven.

[0049] FIG. 4A and 4B illustrate how a slide basket 410 can be positioned on a slide baking device comprising a baking tray 430 having a tray base 432 and a sorbent support 436 so that the sorbent support 436 contacts the exposed slide edges 402b of the slides 402 and separates the exposed slide edges 402b from the basket supports 420 and its shelves 426. Sorbent block 436 has a width W2 that is substantially equal to or smaller than width Wi of the basket opening defined by the basket supports 420 of the slide basket 410. During baking, paraffin from the tissue may be melted, causing it to flow down the slide, as illustrated by conceptual arrows 440 in FIG. 4B. By separating the slide edges 402b from the basket supports 420 and its shelves 426 while baking or heating, flow of melted embedding medium onto the slide basket 410 is reduced or prevented. The slides 402 can be dried, heated and/or baked, without contaminating the slide basket 410 with residual embedding medium. When reaching the absorbent block, the embedding medium can be sorbed by the sorbent support 436. In some embodiments, capillary forces cause the embedding medium to be absorbed. Additionally, the surface tension of the embedding medium may help it move along the slide edge 402b, towards the absorbent block 436, as illustrated by conceptual arrows 442. [0050] The tray base 432 can be configured to removably hold the sorbent support 436 but keep it from moving when the slide basket 410 is lowered onto it or while the basket is in position on it. In some embodiments, the tray base 432 defines a recess 431 configured to receive sorbent support 436. In some embodiments, the sorbent support is integral with the tray base. Sorbent support 436 has a width W2. In some embodiments, the sorbent support is a sorbent block having a substantially rectangular shape with a height, length, and width. In some embodiments, the sorbent block width is less than the width of the basket opening defined by the basket supports of the slide basket. It will be appreciated that the sorbent support or member may have any dimensions consistent with its intended use.

[0051] The slide basket can include protrusions 428 that project upward from basket support 420 into the interior volume of slide basket. The protrusions 428 can keep the slides 402 contained in the slide basket separated from each other. In some embodiments, basket support 420 comprises teeth 429 on a side opposite an interior volume of slide basket and its protrusions 428. The exterior teeth 429 can interact with a track to move the slide basket into and out of various devices.

[0052] In some embodiments, a slide baking apparatus comprises a chamber for receiving a slide basket and heating the slides held in the slide basket. The chamber can be specific for slide baking, or it can be a general heating chamber, such as an oven. In some embodiments, the baking tray 330 may be or include a slide baking device, in which case the upper surface of the tray base 332 may serve as a heating surface. The slide baking device generally may have any configuration effective for generating and transferring heat energy to the upper surface. Thus, for example, the baking tray as a slide baking device may include one or more resistive heating elements (not specifically shown) disposed in or on the base 332 in thermal contact with the upper surface, or disposed directly on upper surface or integral with the upper surface. In an embodiment, the upper surface itself may serve as the heating element. The baking tray 330 may also include a heater voltage source (power supply) providing electrical current to the heating element(s).

[0053] As an alternative (or in addition) to resistive heating elements, the slide baking device may provide one or more radiant heating sources such as, for example, infrared (IR) lamps. Additionally or alternatively, the slide basket may be placed in a heating chamber and a slide baking device may be configured to heat the chamber (i.e., the interior volume of the chamber), whereby the specimen and slides are heated by convection.

[0054] In the embodiment shown herein, the slide baking tray 330, has an open architecture, in that the baking tray 330 may be positioned and operated in an ambient environment, for example on a bench top, tabletop, or the like. Alternatively, the device 300 may include an enclosure or chamber (not shown). Such a chamber may be provided if it is desired to control one or more parameters of the operating environment of the baking process, such as gas composition, pressure, temperature, light intensity, etc.

[0055] Exemplary materials for the baking tray 330 and/or the tray base 332 include thermosetting polymers such as polyetherimide (PEI), polyether ether ketone (PEEK), polytetrafluoroethylene (PTFE) polybenzimidazole (PBI), and polydicyclopentadiene (pDCPD); and metal alloys such as high chrome nickel austenitic alloys, nickel-based alloys, cobalt chrome nickel-based alloys, and molybdenum titanium alloys.

[0056] In some embodiments, a slide baking device comprises one or more recesses, to contain replaceable sorbent support or members, which fit between inside the basket supports of a slide basket, so that it can contact an edge of a slide in the slide basket. The slide baking device should be formed from a heat resistant material with low heat capacity, to prevent the user from burns when removing the slide baking device from the oven. Slides mounted with tissue sections or other specimens are placed in the slide basket. The slide basket is placed on top of one of the sorbent supports causing the slides to be lifted slightly from the bracket supports of the slide basket so that the exposed slide edges of the slides do not contact the basket supports of the slide basket.

[0057] The sorbent support or member can be formed partially or entirely from a material that absorbs an embedding medium. The sorbent support or member can collect some or all of the embedding medium that melts from the embedded specimen and travels to an edge of the slide. The sorbent support or member may be movable, or its position adjustable, relative to the upper (outer) surface of the baking tray or relative to the bottom (basket supports) of the slide basket. The sorbent support or member may be utilized to assist in “wi eking away” the embedding medium as it moves (either by gravity or by being pushed or pulled, or repelled or attracted) to the edge of the slide and contacts the sorbent support or member.

[0058] In some embodiments, the sorbent support or member may be heated to or operate at a higher temperature than that of the (optionally heated) surface of the baking tray to cause the embedding medium to readily flow onto the sorbent support or member as the embedding medium reaches the edge of the slide. In some embodiments, the sorbent support or member may comprise a thermally conductive material and in operation may be heated to assist in removal of the embedding medium, such as by preventing it from solidifying on the slide. Accordingly, in embodiments in which the slide baking apparatus comprises a (main or first) slide baking device, the sorbent support or member may also be referred to herein as an auxiliary or second slide baking device.

[0059] The sorbent support or member can comprise a solid, porous material, for example a zeolite or silica aerogel that will adsorb paraffin or other waxes used as the embedding medium. Silica aerogels can have high porosities and have been used to absorb paraffin oils. In some embodiments, the sorbent support or member comprises an aluminosilicate molecular sieve or zeolite, such as a material having relatively uniform pore diameters of about 5 Angstroms (type 5A molecular sieves or 5A zeolites). In some embodiments, the sorbent support or member comprises a paraffin-sorbing material. In some embodiments, substantially all of the sorbent support or member is a paraffin-sorbing material.

[0060] In some embodiments, sorbent support or member has a width W2. For example, width W2 can be about 10 mm, or 15 mm, or 20 mm, or 23 mm, and any of the foregoing values can be combined to form a range for value of W2. In some embodiments, width W2 is selected based on dimensions of one or more slide baskets for which the slide baking device is configured for use. More particularly, for a slide basket having a basket opening between its basket supports for the slide, the width of the basket opening Wi can be substantially the same as width W2. In some embodiments, width W2 of the sorbent support or member is 0.1 mm, 0.25 mm, 0.5 mm, 0.75 mm, 1 mm, 1.5 mm, 2 mm, or 5 mm less than width Wi; and any of the foregoing values can be combined to form a range for a maximum difference between W2 and Wi.

[0061] Non-limiting embodiments of a method for baking slides having embedded specimen will now be described, using as an example the device 330 described above and illustrated in Figures 3, 4A and 4B. In some embodiments, an embedded specimen is cut or sliced and placed onto a slide.

[0062] It should be appreciated that one or more portions of the present methods and apparatus may be automated rather than performed by a user. In some embodiments, the slide baking apparatus further comprises a controller in signal communication with (by wired or wireless means) a slide baking apparatus or a part thereof, such as a robotic arm, a heating element, or other device. The controller may be, for example, a desktop computer, laptop computer, portable computer, tablet computer, handheld computer, mobile computing device, personal digital assistant (PDA), smartphone, etc., and may include one or more types of hardware (e.g., electronicbased processors, memories, user input peripherals, user output peripherals, etc.), firmware, and/or software.

[0063] The slide baking apparatus may also include other electronics (not shown) configured for controlling the baking procedure. Thus, for example, the slide baking device may include an ON/OFF switch configured for controlling the ON/OFF state of the heating element. The electronics of the slide baking apparatus may be arranged in a console on a chamber, or in a separate console.

[0064] In some embodiments, the present methods and apparatus are employed for removing a desired amount of embedding medium from an embedded specimen or for deparaffinization. That is, the present methods and apparatus can be employed to deliberately remove some or all of the embedding medium from an embedded specimen on a slide, as opposed to removing embedded medium that incidentally melts and separates from an embedded specimen during slide baking. Such methods can also comprise applying one or more solvents to the embedded specimens on the slides, such as xylene, xylene substitutes or toluene. The solvents can be applied before or after the embedded specimens are heated using the present slide baking apparatus.

[0065] In some embodiments, the present methods and apparatus do not remove a significant amount of embedding medium from the embedded specimens. The embedding medium may be desirable for preventing the specimen from deteriorating or being compromised during storage.

[0066] In some embodiments, the embedded specimens are heated to a baking temperature. Exemplary baking temperatures include temperatures of at least about 35°C, or at least about 40°C, or at least about 50°C, or at least about 60°C; exemplary baking temperatures also include temperatures of at most about 120°C, or at most about 100°C, at most about 80°C, or at most about 70°C; it is contemplated that any of the foregoing minima and maxima can be combined to form a range. In some embodiments, the embedded specimens are heated for a baking period.

[0067] In the embodiments described and illustrated thus far, the embedded specimens and the slide have been depicted primarily as being vertically oriented. FIGs. 3, 4A and 4B illustrate examples of utilizing a slide baking apparatus to bake embedded specimens onto slides in a vertically orientation. Orienting the embedded specimen vertically, at some other angle to the vertical, may promote removal of the embedding medium through the assistance of gravity. However, it is also contemplated that the slides and embedded specimens can be oriented horizontal (ninety degrees relative to a vertical reference plane), or at any other angle between the horizontal and vertical reference planes (e g., in a range from zero degrees to ninety degrees relative to a horizontal reference plane).

[0068] Various other embodiments of a slide baking apparatus encompassed by the present disclosure may include combinations of features from different embodiments described above and illustrated in the Figures.

EXEMPLARY EMBODIMENTS

[0069] Exemplary embodiments provided in accordance with the presently disclosed subject matter include, but are not limited to, the following:

To be added when claims are finalized

[0070] It will be understood that various aspects or details of the invention may be changed without departing from the scope of the invention. Furthermore, the foregoing description is for the purpose of illustration only, and not for the purpose of limitation, as the present invention is defined by the claims.

Claims

CLAIMS What is claimed is:

1. A method for baking a plurality of slides having embedded specimens on slides, the method comprising: inserting one or more slides into a slide basket configured to hold a plurality of the slides, wherein each of the inserted slides has an embedded specimen on a surface of the slide, wherein the slide basket has one or more basket supports configured to contact a slide edge of the slides while defining a basket opening that exposes the slide edge; positioning the slide basket on a slide baking device comprising a sorbent support so that the sorbent support contacts the exposed slide edge of one or more of the slides and separates the exposed slide edges from the basket supports; and heating the slides having the embedded specimens while in the slide basket and while the slide edges are separated from the one or more basket supports, thereby reducing or preventing flow of melted embedding medium onto the slide basket.

2. The method of claim 1 , wherein the slides are heated for a baking period sufficient to adhere the embedded specimens onto the surfaces of the slides.

3. The method of claim 1 or claim 2, wherein the basket supports are configured to support slides having a width Ws, and the basket opening defined by the basket supports has a width from 1% to 10% less than Ws.

4. The method of any of claims 1 to 3, wherein the surfaces of the slides are substantially vertical when held in the slide basket, or at an angle between about 70 degrees and about 90 degrees relative to a plane of the basket supports, or a horizontal plane of the ground or a baking tray.

5. The method of any of claims 1 to 4, wherein the slide basket is configured to hold the slides so that the slide surfaces are substantially vertical, and/or a short edge is supported by the one or more basket supports.

6. The method of any of claims 1 to 5, wherein the sorbent support is on a baking tray.

7. The method of claim 6, wherein the sorbent support is integral with the baking tray.

8. The method of claim 6, wherein the sorbent support is removable from the slide baking tray.

9. The method of claim 6 or claim 8, wherein the baking tray comprises one or more recesses for receiving the sorbent support.

10. The method of any of claims 6, 8 or 9, wherein the method further comprises replacing the sorbent support after baking one or more slide basket.

11. The method of any of claims 6 to 10, wherein the baking tray comprises a heating element.

12. The method of any of claims 1 to 11, wherein heating the slides comprises heating the slides to a temperature below a melting point of the embedding medium.

13. The method of any of claims 1 to 11, wherein the heating is at a temperature above a melting point of the embedding medium.

14. The method of any of claims 1 to 13, further comprising robotically moving the slide basket onto the sorbent support.

15. The method of any of claims 1 to 14, further comprising: robotically moving the slide baking device into a chamber; heating the slides in the chamber; robotically removing the slide baking device from the chamber after a baking period.

16. A slide baking device for baking a plurality of slides having embedded specimens on the slides, the device comprising: a baking tray comprising a tray base, and a sorbent support, wherein the tray base is configured to hold the sorbent support.

17. The slide baking device of claim 16, wherein the sorbent support is a sorbent block having a substantially rectangular shape with a height, length, and width.

18. The slide baking device of claim 17, wherein the sorbent block width is less than the width of the basket opening defined by the basket supports of the slide basket.

19. The slide baking device of claim 17 or claim 18, wherein the sorbent support comprises a solid, porous material.

20. The slide baking device of any of claims 16 to 19, wherein the sorbent support comprises a zeolite or silica aerogel.

21. The slide baking device of any of claims 16 to 20, wherein the sorbent support comprises a paraffin-sorbing material.

22. The slide baking device of claim 21, wherein substantially all of the sorbent support is a paraffin-sorbing material.

23. The device of any of claims 16 to 22, wherein the tray base is configured to removably hold the sorbent support.

24. The device of claim 23, wherein the tray base comprises a recess configured to receive the sorbent support.

25. The device of any of claims 16 to 22, wherein the sorbent support is integral with the tray base.

26. The device of any of claims 16 to 25, wherein the baking tray further comprises a tray bracket extending from the tray base, such as two tray brackets extending in a substantially perpendicular direction.

27. The device of any of claims 16 to 26, wherein the baking tray comprises a heating element configured to supply heat in an environment around the sorbent support.

28. A slide baking apparatus comprising the slide baking device of any of claims 16 to 27 and a heating chamber comprising a heating element to supply heat to an interior volume of the chamber, and the interior volume of the chamber is a size sufficient to receive the baking tray and one or more slide baskets positioned on the baking tray.

29. The slide baking apparatus of claim 28, further comprising a robotic arm that engages a bracket on the baking tray and moves the baking tray into and out of the heating chamber.

30. A method of reducing contamination of a slide basket with melted embedding medium, wherein said slide basket comprises at least one slide having a tissue section embedded in said embedding medium thereon, said method comprising: placing a bottom surface of said at least one slide in contact with a sorbent member under conditions where said embedding medium melts and flows toward said bottom surface of said slide, wherein said melted embedding medium is sorbed by said sorbent member.

31. The method of claim 30, wherein said sorbent member causes said bottom surface of said at least one slide to be lifted above a basket support of said slide basket when said sorbent member contacts said bottom surface of said at least one slide.

32. The method of any of claims 30 to 31 wherein said sorbent member is an absorbent member.

33. The method of any of claims 30 to 32, wherein said embedding medium is paraffin.

34. The method of any of claims 30 to 33, wherein said sorbent member is configured to fit within a space defined by said basket support.

35. The method of any of claims 30 to 34, further comprising heating said at least one slide for a baking period sufficient to adhere an embedded specimen onto a surface of said at least one slide.

36. The method of any of claims 30 to 35, wherein the slide basket is configured to support slides having a width Ws, and the slide basket has a basket opening having a width from 1% to 10% less than Ws.

37. The method of any of claims 30 to 36, wherein the surfaces of the slides are substantially vertical when held in the slide basket, or at an angle between about 70 degrees and about 90 degrees relative to a plane of the basket supports, or a horizontal plane of the ground or a baking tray.

38. The method of any of claims 30 to 37, wherein the slide basket is configured to hold the slides so that the slide surfaces are substantially vertical, and/or a short edge is supported by the one or more basket supports.

39. The method of any of claims 30 to 38, wherein the sorbent member is on a baking tray.

40. The method of claim 39, wherein the sorbent member is integral with the baking tray.

41 . The method of claim 39, wherein the sorbent member is removable from the baking tray.

42. The method of claim 39 or claim 41, wherein the baking tray comprises one or more recesses for receiving the sorbent support.

43. The method of any of claims 39, 41 or 42, wherein the method further comprises replacing the sorbent member after baking one or more slide basket.

44. The method of any of claims 39 to 43, wherein the baking tray comprises a heating element.

45. The method of any of claims 30 to 44, further comprising heating said at least one slide to a temperature below a melting point of the embedding medium.

46. The method of any of claims 30 to 44, further comprising heating said at least one slide to a temperature above a melting point of the embedding medium.

47. The method of any of claims 30 to 46, further comprising robotically moving the slide basket onto the sorbent support.

48. The method of any of claims 30 to 47, further comprising: robotically moving the slide baking device into a chamber; heating the slides in the chamber; robotically removing the slide baking device from the chamber after a baking period.

49. A slide baking tray comprising a base having at least one sorbent member thereon, wherein said slide baking tray is configured to receive melted embedded medium from a slide when said slide baking tray is placed adjacent to a slide holding device comprising said slide.

50. The slide baking tray of claim 49, wherein said slide baking tray is configured to fit within an opening in said slide holding device.

51. The slide baking tray of any of claims 49 to 50, wherein said slide holding device is a slide basket.

52. The slide baking device of any of claims 49 to 51, wherein at least one sorbent member is a sorbent block having a substantially rectangular shape with a height, length, and width.

53. The slide baking device of claim 52, wherein the sorbent block width is less than the width of an opening defined by said slide holding device.

54. The slide baking device of any of claims 49 to 53, wherein said at least one sorbent member comprises a solid, porous material.

55. The slide baking device of any of claims 49 to 54, wherein said at least one sorbent member comprises a zeolite or silica aerogel.

56. The slide baking device of any of claims 49 to 55, wherein said at least one sorbent member comprises a paraffin-sorbing material.

57. The slide baking device of claim 56, wherein substantially all of said at least one sorbent member is a paraffin-sorbing material.

58. The device of any of claims 49 to 57, wherein said slide baking tray is configured to removably hold said at least one sorbent member.

59. The device of claim 58, wherein said slide baking tray comprises a recess configured to receive said at least one sorbent member.

60. The device of any of claims 49 to 59, wherein said at least one sorbent member is integral with said slide baking tray.

61. The device of any of claims 49 to 60, wherein said slide baking tray further comprises a tray bracket extending from said slide baking tray, such as two tray brackets extending in a substantially perpendicular direction.

62. The device of any of claims 16 to 26, wherein said slide baking tray comprises a heating element configured to supply heat in an environment around said at least one sorbent member.