Patent Publication Number: US-2021172969-A1

Title: Automated slide processing systems, consumable slide processing modules, and reagent cartridges

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application is a continuation of PCT Application No. PCT/EP2019/068814, filed Jul. 12, 2019, which claims priority to U.S. Provisional Application No. 62/698,820, filed Jul. 16, 2018, which are hereby incorporated by reference in their entireties. 
    
    
     TECHNICAL FIELD 
     This disclosure relates to systems for preparing samples for analysis. In particular, the disclosure relates to automated slide processing systems, consumable slide processing modules, and related technologies for processing samples. 
     BACKGROUND 
     A wide variety of techniques have been developed to prepare and analyze biological specimens. Example techniques include microscopy, microarray analyses (e.g., protein and nucleic acid microarray analyses), and mass spectrometric methods. Specimens are typically prepared for analysis by applying one or more liquids (e.g., reagents) to the specimens. If a specimen is treated with multiple liquids, both the application and subsequent removal of each liquid can be important for producing stained specimens suitable for analysis. For example, microscope slides bearing biological specimens, e.g., tissue sections or cells, are often treated with a series of manually applied reagents to add color and contrast to otherwise transparent or invisible cells or cell components. This labor-intensive process often results in inconsistent processing due to individual techniques among laboratory technicians. 
     Automated slide processing machines are often used for high-volume slide processing. Unfortunately, conventional automated slide processing machines are typically relatively large, thus making them unsuitable for use in surgery suites and small laboratories. For example, conventional automated pipetting systems can be quite large and have pipetting heads capable of individually dispensing liquids onto specimen-bearing microscope slides held by a tray. Pipettes are used to aspirate reagents out of bottles and to dispense the reagents onto uncovered slides. The reagents are exposed to air which can lead to degradation, e.g., due to oxidation, or biologic contamination of solution components over time. This can lead to inconsistent staining unless the solutions are regularly replenished or exchanged. Replenishing or exchanging liquids can be a time-consuming and wasteful process that often disrupts work-flow. Additionally, automated pipetting systems have a limited number of reagent bottles, thus limiting the number of staining protocols that can be performed or necessitating swapping which negatively impacts workflow. Accordingly, conventional automated slide processing machines suffer various drawbacks. 
     SUMMARY 
     At least some embodiments include a staining system for preparing and analyzing biological specimens. The staining system can include a consumable stainer unit for processing microscope slides bearing biological specimens with a series of robotically applied reagents to add color stains and background contrast to otherwise transparent or invisible cells or cell components. The stainer unit can be used with an instrument in a laboratory environment. The instrument can cause reagent to be delivered from reagent-filled capsules to a cell to process a specimen. The cell can be a flow or reaction cell that prevents, limits, or minimizes reagent boiling, evaporative losses, stain degradation (e.g., due to oxidation), and minimizes or eliminates the possibility of tissue cross-contamination, or other problems. Accordingly, the stainer unit can be used to control reagent characteristics (e.g., concentrations, mixtures, etc.) to enhance the effectiveness of the reagents, resulting in desired staining characteristics. In single-use embodiments, the reagent cartridge can hold enough reagent to perform a single multistep staining protocol to avoid reagent waste and can be made of relative low-cost materials. To process multiple slides, each slide can be processed with a consumable stainer unit selected from a family of consumables based on the reagents stored within them, and the staining protocol required. Manual procedures, automated procedures, or combinations of manual and automated procedures can be used to process the slides. 
     In some embodiments, a stainer unit includes reagents and a reaction cell configured to at least partially define a reaction chamber. The stainer unit can include a fluid circuit that allows the reagents to be delivered to the reaction chamber. The fluid circuit can seal the reaction cell to inhibit or prevent evaporation and/or boiling of one or more of the reagents in the reaction chamber during, for example, high-temperature processing. The fluid circuit can include one or more valves in fluid communication with the reaction chamber. The valves can be located along passageways in fluid communication with the reaction chamber. In some embodiments, the fluid circuit allows the regents to be sequentially delivered to the reaction chamber and inhibits or prevents fluid flow away from reaction chamber. The sealed reaction cell can increase a boiling point of the reagent to accelerate high-temperature target retrieval (e.g., antigen retrieval). The reaction chamber can be located along a specimen-bearing surface of a microscope slide or at another suitable location, and the reaction cell can be a flow cell through which reagents can flow and be held in contact with the specimen. 
     In some embodiments, an automated slide staining system includes a high-temperature slide processing module. The slide processing module can include regents, a reaction cell configured to at least partially define a reaction chamber along a specimen-bearing surface of a microscope slide that is carried by the high-temperature slide processing module, and one or more valves. The valves allow the reagents to be delivered to the reaction chamber. The valves are configured to seal the reaction cell to inhibit boiling of one or more of the reagents in the reaction chamber. When the reaction cell is sealed, the reaction chamber can be pressurized to raise a boiling point of one of the reagents in the reaction chamber for high temperature antigen retrieval. In some embodiments, regents can be sequentially delivered to the reaction chamber and can inhibit fluid from flowing out of the reaction chamber, thereby increasing the reagent&#39;s boiling point. The valves can include a first valve in communication with an inlet port of the flow cell and a second valve in communication with an outlet port of the flow cell and a waste container. 
     In further embodiments, a microfluidic slide processing module for processing slides includes a support base and a flow cell connected to the support base. The flow cell can include a slide engagement region having a surface and a sealing member. The sealing member is configured to sealingly contact a specimen-bearing surface of a microscope slide to define a flow cell between the surface of the slide engagement region and the specimen-bearing surface. In some embodiments, the flow cell can be sealed by one or more valves (e.g., valves positioned along entry and exit ports, fluid lines, or passageways), and the sealing arrangement provided via the reaction chamber seals. Reagents can be held in the reaction chamber to maintain hydration of the specimen and provide a suitable target with associated marker, e.g., an antibody, DNA probe, dye molecule, or the like. The microfluidic slide processing module, including the sealed reaction chamber, can then be heated to temperatures higher than the boiling temperature of the reagent (e.g., a primarily water based reagent) to provide enhanced antigen retrieval. The flow cell area can be provided with suitable physical support on upper and lower surfaces to ensure seals are maintained even when high pressure is experienced. Such high pressures can inhibit or prevent boiling when the reagent is at temperatures equal to or higher than 80° C., 90° C., 100° C., 105° C., 110° C., 115° C., or 120° C. such that enhanced staining (e.g., accelerated processing) can be achieved in very short periods of time. Fresh reagent can be pumped through an open inlet valve and into the reaction chamber while used reagent is pushed through an open outlet valve. The inlet and outlet valves can be closed again to perform additional high temperature steps. 
     In yet further embodiments, an automated staining system can include a slide processing module and a dispensing instrument. The slide processing module can include a flow cell configured to sealingly contact a specimen-bearing surface of a microscope slide to provide a reaction chamber along the specimen-bearing surface, a capsule receiver fluidly coupled to the flow cell and including a chamber, and a reagent cartridge that holds a plurality of capsules each containing reagent. The reagent cartridge sequentially feeds the capsules to the capsule receiver. The dispensing instrument can operate to cause a respective one of the capsules (or multiple capsules to mix reagents) that has been delivered to the chamber to release reagent such that the released reagent is delivered to the reaction chamber. 
     The dispensing instrument can include a reciprocating drive mechanism operable to move the actuator in a first direction to cause the respective one of the capsules located with the chamber to release reagent and a second direction to allow another one of the capsules to be delivered into the chamber. The actuator can be fixedly coupled to or part of the dispensing instrument. In some embodiments, the dispensing instrument can include a drive mechanism having a dispensing mode for moving the actuator toward the respective one of the capsules in the chamber and a reloading mode for allowing another one of the capsules filled with reagent to be delivered into the chamber. Two capsules can be burst to produce reagent mixtures. 
     A method for processing a specimen includes robotically releasing a series of reagents from a plurality of capsules such that the reagents flow into a reaction chamber of a flow cell such that the reagents sequentially contact a specimen held on a microscope slide cartridge and in the reaction chamber. The reaction chamber can be at least partially defined by a mounting surface of a microscope slide and a microscope slide cartridge. The method can include causing reagent in the reaction chamber to flow into at least one waste container of the microscope slide cartridge. A first reagent can be delivered from a first one of the capsules to the reaction chamber, and a wash liquid can be delivered to the reaction chamber to flush the first regent from the reaction chamber. After flushing the reaction chamber, additional reagents from the other capsules can be delivered, whether sequentially or concurrently, to the reaction chamber. In some flushing procedures, the wash liquid can remove most of a reagent by volume from the reaction chamber. In some dispensing procedures, a plunger is repeated reciprocated between a standby position and a dispense position to cause reagent to be released each of the reagent capsules. 
     In further embodiments, a method includes performing a plurality of specimen processing operations on a specimen held in a flow cell at least partially defined by a mounting surface of a slide carrying the specimen. The processing can include sequentially delivering reagents to a reaction chamber of the flow cell. The used reagent can be delivered into a waste container fluidly coupled to the flow cell. The microscope slide cartridge can carry the microscope slide while the microscope slide cartridge is removed from and/or delivered to an automated instrument. Each reagent can be delivered through a fluid circuit of the microscope slide cartridge to deliver reagent into the reaction chamber and to deliver waste reagent to waste container. 
     In further embodiments, a method includes processing a plurality of specimens within the same cartridge. The processing can include applying the same reagents to multiple specimens either simultaneously or sequentially. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  is a front view of an automated specimen processing system in accordance with an embodiment of the disclosed technology. 
         FIG. 2  is a front view of internal components of the specimen processing system of  FIG. 1 . 
         FIG. 3  is a block diagram of an automated specimen processing system with processing zones in accordance with an embodiment of the disclosed technology. 
         FIG. 4  is a plan view of an automated specimen processing system in accordance with an embodiment of the disclosed technology. 
         FIG. 5  is a perspective view of a slide processing module in accordance with an embodiment of the disclosed technology. 
         FIG. 6  is a perspective view of the slide processing module of  FIG. 5  with a flow cell in an open configuration. 
         FIG. 7  is a plan view of the processing module in accordance with an embodiment of the disclosed technology. 
         FIG. 8  is a detailed cross-sectional view of a portion the processing modules of  FIG. 7 . 
         FIG. 9  is a detailed cross-sectional view of a dispensing unit of  FIG. 7  in accordance with an embodiment of the disclosed technology. 
         FIG. 10  is a detailed cross-sectional view of the dispensing unit after multiple capsules have released reagent. 
         FIG. 11  is a flow chart illustrating a method for processing a specimen in accordance with an embodiment of the disclosed technology. 
     
    
    
     DETAILED DESCRIPTION 
     The following description of several embodiments describes non-limiting examples of the disclosed system and methods to illustrate the technology. Furthermore, all titles and headings provided herein are for convenience only and are not intended to limit or interpret the scope or meaning of the invention. Specific details of several embodiments of the present technology are disclosed herein with reference to  FIGS. 1-11 . It should be noted that other embodiments in addition to those disclosed herein are within the scope of the present technology. For example, embodiments of the present technology can have different configurations, components, substances, and/or procedures than those shown or described herein. Moreover, a person of ordinary skill in the art will understand that embodiments of the present technology can have configurations, components, substances, and/or procedures in addition to those shown or described herein and that these and other embodiments can be without several of the configurations, components, and/or procedures shown or described herein without deviating from the present technology. 
     I. Overview of Automated Processing Systems 
       FIG. 1  is a front view of an automated specimen processing system  100  (“system  100 ”) in accordance with an embodiment of the disclosed technology. The system  100  can include a robotic staining instrument  110  and consumable stainer units  108   a ,  108   b . The staining instrument  110  can include a protective housing  120 , a loading zone or loading station  124  (“station  124 ”), and a controller  130 . The station  124  can include a door or access port  146  for loading and unloading stainer units  108   a ,  108   b , illustrated schematically, carrying specimen-bearing microscope slides. Each stainer unit  108   a ,  108   b  can contain reagents and a waste container. The staining instrument  110  can use reagents on-board the stainer units  108  to process the specimens. After processing, the stainer units  108   a ,  108   b  can be retrieved from the instrument  110 , the specimen-bearing slides can be removed from the stainer units  108   a ,  108   b , and the specimens can be analyzed. The system can be provided with storage capability, for example a stainer unit holding rack from which the system can access stainer units to be processed, and capable of re-inserting stainer units at various stages of assay completion. 
     Each stainer unit  108   a ,  108   b  (collectively “stainer units  108 ”) can contain most or all of the substances for performing the assay, for example, specimen conditioning (e.g., cell conditioning, washing, etc.), antigen/target retrieval, staining (e.g., hematoxylin and eosin staining), or other types of protocols (e.g., immunohistochemistry protocols, in situ hybridization protocols, etc.) for preparing specimens for visual inspection, fluorescent visualization, microscopy, microanalyses, mass spectrometric methods, imaging (e.g., digital imaging), or other analytical or imaging methods. The fluids can be held in airtight capsules, sealed reservoirs, containers, or other suitable holders to minimize or limit the possibility of reagent oxidation that could impact staining even when the stainer unit is stored for relatively long periods of time (e.g., months or years). The single doses also limit thermal exposure to other stored reagents when taken out of temperature controlled environments (e.g., when removed from a refrigerator). The stainer units  108  can include one or more cells (e.g., flow cells, reaction cells, etc.), reaction chambers, fluid lines, channels, valves (e.g., check valves, membrane valves, globe valves, etc.), ports, pressurization devices (e.g., pumps, syringes, etc.), or other components for fluidly communicating with reaction chambers. The stainer units  108  can also include one or more mixing components (e.g., mixing wells, reagent trays, etc.) for mixing reagents in, for example, lyophilized and/or liquid form. The configurations of the stainer units and onboard substances can be selected based upon the staining protocols to be performed and functionality of the staining instrument  110 . 
     Multiple stainer units can be available to perform different protocols. For example, the stainer unit  108   a  can have reagents for performing hematoxylin and eosin (H&amp;E) staining and the stainer unit  108   b  can have reagents for performing advanced staining protocols, such as immunohistochemistry protocols or in situ hybridization protocols. In some single-use embodiments, each stainer unit  108  can carry a sufficient amount of reagent to perform only a single protocol using fresh reagents to avoid producing excess reagent waste. The reagent reservoirs and waste containers can be permanently sealed to prevent reuse. In some multi-use embodiments, reagent can be replenished any number of times and the reagent chamber can be flushed and washed. The stainer units  108  can contain waste materials for convenient disposal. The waste materials can include waste reagents, wash solutions, or other fluids that can be collected in a removable waste container that can be discarded separately from other components of the stainer unit  108 . This allows for separate handling of unused and used liquids. 
     The controller  130  can be used to select protocols and can receive information. The information can be inputted by the user using an input device  131 , such as a keyboard, a touchscreen, or the like. In some embodiments, the staining instrument  110  includes one or more readers in communication with the controller  130 . The readers can obtain information from machine readable labels, barcodes, or other types of labels applied to, for example, the microscope slides, stainer units, or reagent reservoirs. The controller  130  can command system components based, at least in part, on the obtained information, and can generally include, without limitation, one or more processors, computers, central processing units, microprocessors, digital signal processors (DSPs), application-specific integrated circuits (ASICs), readers, or the like. In some embodiments, the controller  130  can be programmed to receive information from microscope slides, process specimens based on the received information, and acquire one or more images of processed specimens. 
     To store information, the controller  130  can include, without limitation, one or more storage elements, such as memory (e.g., volatile memory, non-volatile memory, read-only memory (ROM), random access memory (RAM)). For example, the memory can be non-transitory computer-readable memory that stores instructions that, when executed by a processor, cause the controller  130  to perform operations. The stored information can include, without limitation, reagent information, expiration information (e.g., reagent expiration date), stainer unit information, staining protocols, reagent recipes, heating or cooling programs, optimization programs, calibration programs, indexing programs, databases, imaging programs, and/or executable programs. The protocols can include reagent protocols (e.g., number and/or order of reagents applied), thermal protocols (e.g., heating/cooling routines), and other executable instructions for processing slides. The stored information can be used to determine, for example, protocols for processing the stainer unit based on information acquired from the stainer unit, inputted by an operator, or both, for example. In some embodiments, the instrument  110  can obtain information from the stainer unit and additional information from the microscope slide. The microscope slide information can include tissue information and staining to be performed. Based on that information, the controller  130  can determine an appropriate protocol for processing the tissue specimen based on the available resources, and if another stainer unit or reagent cartridge should be used, a notification can be provided to the user. 
     In operation, a user can manually load the stainer unit  108  with a specimen-bearing microscope slide. The user can visually confirm proper loading and can then feed the stainer unit  108  to the instrument  110 . In other embodiments, the user separately loads microscopes slides and stainer units  108  into the staining instrument  110 , which can robotically load the stainer units with the microscope slides. Reagent cartridges can be installed in the stainer units  108  before or after delivering the units to the staining instrument  110 . Closed reagent reservoirs or capsules can prevent, limit, or minimize evaporative losses, stain degradation, cross-contamination between slides (typically experienced with dip and dunk systems), or other problems, thereby enabling control of reagent characteristics (e.g., concentrations, mixtures, etc.) to enhance the effectiveness of the reagents and resulting in desired staining characteristics. The sealed reagent chambers of the closed flow cell can be pressurized to inhibit or prevent boiling of the reagent or water in the specimen, thereby enabling high temperature processing without the adverse effect associated with excessive heating the reagent and/or specimen. 
     The staining instrument  110  can controllably dispense fresh processing liquids onto the slides without splattering onto its mechanical or electrical components, as well as adjacent slides often present in conventional pipetting systems, and can controllably remove processing liquids from the slides via vacuum or liquid replacement or other suitable means. The controlled reagent dispensing/removal reduces volumes of liquid waste (e.g., waste reagents which have passed through the reaction chamber) by, for example, minimizing or otherwise limiting volumes of utilized reagents. In some embodiments, specimen processing may include contacting specimens with a series of liquids that include, for example, one or more deparaffinizing liquids, conditioning liquids, staining reagents, stain-differentiating reagents, stain-setting reagents, washing liquids, and/or coverslipping liquids. 
     The stainer units  108  can contain the reagents throughout processing, so the staining instrument  110  can process specimens without contacting the reagents. For example, the stainer units  108  can hold aliquots of reagent and can cause reagents to flow into a reaction chamber and into contact with a specimen. In some procedures, most of the reagent from multiple capsules or reservoirs is delivered to the flow cell to process the specimen. Most of the reagent, by volume, can be contained in the stainer units  108  is carried in a waste container upon completion of the specimen processing operations. For example, the waste container can contain most of the reagent, by weight or volume, carried by the used stainer unit  108 . In some procedures, the waste container contains at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, and 95% of the total volume of reagent carried by the stainer unit  108 . The used stainer unit  108 , which still carries the unused reagents and waste reagent, can be removed from the instrument  110  for subsequent disposal. 
     Closed reagent chambers can prevent, limit, or minimize boiling of reagents, boiling of tissue, evaporative losses, stain degradation, cross-contamination between slides (typically experienced with dip and dunk systems), or other problems, thereby enabling control of reagent characteristics (e.g., concentrations, mixtures, etc.) to enhance the effectiveness of the reagents and resulting in desired staining characteristics. The stainer units  108  can have integrated coverslips for viewing the specimen, thereby avoiding an additional coverslipping step. In some embodiments, the staining instrument  110  can perform a coverslipping operation. After coverslipping, the stainer unit  108 , which carries the coverslipped slide, can be retrieved at the station  124 . In other embodiments, the microscope slide can be coverslipped after removal from the instrument  110 . Additional processing can be performed on the slide. 
       FIG. 2  is a front view of internal components of the instrument  110  in accordance with an embodiment of the disclosed technology. The instrument  110  can include a dispenser instrument  160  configured to operate a processing module  108 , illustrated at a module-receiving station  125 . The processing module  108  can be include a base  200 , a dispensing unit  204 , and a reaction or flow cell  210 . The base  200  can include fluid components for delivering reagents to the flow cell  210  and can be a rigid or semi-rigid plate. The dispenser instrument  160  can operate the dispensing unit  204  to deliver, or cause to be delivered, reagents to the flow cell  210 . Dispensing units are discussed in connection with  FIG. 5-9 . 
     The dispenser instrument  160  can include one or more actuators for bursting reagent-filled capsules, piercing reagent-filled capsules, operating syringes, or other components of the dispensing unit  204 . For example, the dispenser instrument  160  can include a reciprocating drive mechanism  205  operable to move an actuator  207  in first direction to cause the respective a capsule located with the dispensing apparatus  204  to release reagent and a second direction to allow another one of the capsules to be delivered into the chamber, as discussed in connection with  FIGS. 9-10 . 
     The flow cell  210  can be a microfluidic cell capable of holding small volumes of liquid. This allows all or most of the reagents, by volume or weight, to be carried onboard the stainer unit  108 . For example, microfluidic flow cells can hold less than, for example, about 25 μL, about 50 μL, about 100 μL, about 150 μL or about 200 μL. In some embodiments, the flow cell  210  can hold about 25 μL to about 100 μL, about 50 μL to about 120 μL, about 75 μL to about 120 μL or other desired volumes. The specimen and reagent can be heated to a temperature equal to or higher than about 60° C., about 70° C., about 80° C., about 90° C., about 100° C., about 110° C., or about 120° C. In some embodiments, the instrument  110  operates to apply heat to the specimen to provide a dwell temperature equal to or less than about 60° C., about 70° C., about 80° C., about 90° C., about 100° C., about 110° C., or about 120° C. for a period of time. The period of time can be equal to or less than about 10 minutes, about 15 minutes, or about 20 minutes. In some embodiments, the flow cell  210  generates thermal energy to heat the specimen and/or reagents and can also operate to cool the sample. Such flow cell  210  can include one or more thermal elements, such as Peltier devices. In some procedures, the reagent can be in liquid form and comprises mostly water by weight. The closed flow cell  210  is sealed to prevent boiling of the liquid reagent therein when the liquid reagent is heated to a temperature equal to about 110° C., about 115° C., or about 110° C. The volume of reagent delivered into the flow cell  210  can be increased to increase the pressure and boiling point of the reagent. 
     The flow cell  210  can contact the mounting surface of the slide to form a fluid-tight seal that is maintained throughout processing even when heat is applied to the specimen and the reagent, with a dwell at 100° C., 110° C., 120° C. for up to about 20 minutes. The liquid reagent, such as primarily water based reagents, can be heated to temperatures higher than their normal boiling points to provide enhanced antigen/target retrieval. The flow cell area can be isolated by one or more seals (e.g., air-tight seals, fluid-tight seals, etc.) that can be maintained even when high pressures are experienced. This ensures that the reagents do not boil when the reagent is a temperature equal to or higher than 80° C., 90° C., 100° C., 105° C., 110° C., 115° C., or 120° C. The high-temperature processing enables enhanced staining in very short times. In some embodiments, the stainer units have pressurizable flow cells for high-temperature target retrieval (e.g., antigen retrieval). To raise the boiling point of the reagent and/or specimen, one or more valves can seal the reaction chamber by inhibiting or preventing the flow of fluid out of the reaction chamber, thereby raising a boiling point of the reagent. For example, the reaction chamber can be closed and pressurizable to raise the boiling point of the reagent (e.g., a reagent with a suitable target/antibody with associated marker) at least about 5%, 10%, 20%, or 30%. 
     The flow cell  210  can also remain sealed during processing to limit or prevent specimen loss, air bubble formation, or other problems, such as measurable evaporative losses. Thermal energy can be delivered uniformly or non-uniformly across the slide via conduction to produce a substantially uniform temperature profile along a specimen-bearing portion of the slide surface. In some embodiments, the substantially uniform temperature profile has a temperature variation equal to or less than a selected temperature variation across the specimen-bearing surface to achieve acceptable stain variation intensity. Non-uniform temperature profiles can also be produced along the slide or specimen if desired. 
     In some IHC protocols, multiple rinses at temperatures in a range between about 20° C. and about 70° C. can be applied. The rinses can include, without limitation, hydrophobic substances and organic solvents. Multiple dispense and removal steps can be performed. Each step can be performed at temperatures in a range of about 20° C. to about 70° C. and can utilize predetermined amounts of multiple reagents. The reagents can be combined prior to tissue contact. During a dwell period, the reagents within the flow cell can cover the entire specimen and, in some embodiments, can be agitated to achieve suitable staining performance. The sample can then be dehydrated and a coverslipping agent can be applied to the slide. A coverslip can be applied and the coverslipping agent can be heated to a suitable curing temperature (e.g., 70° C., 80° C., 90° C., or another suitable temperature). Alternatively, the flow cell can have an integrated coverslip. The stainer unit can allow visual access to both sides of the slides for automated imaging and visual inspection of the specimen. 
     The instrument  110  can perform one or more washing cycles to add and subsequently wash reagents from the flow cell  210 . After incubation, reagent can be washed from the flow cell  210  to remove unreacted reagent that could affect a subsequent processing step. A washing cycle can include flushing the flow cell  210  with an excess of buffer or wash solution. The unreacted reagent can be diluted with the excess volume of the buffer or wash solution and driven out of the flow cell. In some embodiments, a washing cycle can include flushing the flow cell  210  with the wash solution. The wash solution could be miscible or immiscible with the prior reagent. In some embodiments, a washing cycle can include flushing the flow cell with a gas (e.g. air). In some protocols, a washing cycle can be performed for fluid exchange after each incubation. 
     The instrument can include a transporter apparatus  172  and an end effector  162 . The transporter apparatus  172  can include, without limitation, one or more rail assemblies, robotic handlers, X-Y-Z transport systems, conveyors, drive elements  176  (e.g., actuators, drive motors, or the like), or other automated mechanisms or components. The end effector  162  can include, without limitation, one or more grippers, clamps, valve actuators (e.g., pushers for opening and closing diaphragm valves), or other components for operating processing modules, controlling liquid delivery, or the like. The configuration and functionality of the end effector  162  can be selected based on the configuration of the processing module  108   a.    
     The stainer unit  108  can include a closure device  260  (e.g., a clamp) that applies pressure to the microscope slide, flow cell  210 , etc. For example, the closure device  260  can apply sufficient pressure to a backside of a microscope slide to maintain a seal at the front side of a downwardly facing slide. By way of another example, the closure device  260  can apply pressure to a cover overlying the front side of an upwardly facing slide. The slide can be a generally rectangular piece of a transparent material having a front side or face for receiving the specimen. The slide can have a length of about 75 mm (3 inches), a width of about 25 mm (1 inch), and a thickness of about 1 mm (0.04 inch) and, in certain embodiments, may include a label and such a label can include characters and/or other machine-readable codes such as a barcode or an RFID tag. In other embodiments, information can be etched into the microscope slide or included within the microscope slide. Other dimensions are also possible. The microscope slide can be a standard microscope slide made of glass without any label. The stainer unit  108   a  and/or slide can be held at a substantially horizontal orientation. The term “substantially horizontal” generally refers to an angle within about +/−5 degrees of horizontal, for example, within about +/−2 degrees of horizontal, such as within about +/−1 degree of horizontal or about +/−0.5 degree of horizontal. The horizontal orientation of the slide can help keep the specimens centered on the slide. The slide can be held at other orientations and positions. The flow cell  210  can be configured to hold other types of substrates capable of carrying specimens in the form of cytological preparations, micro-arrays, tissue arrays, or the like. 
     The biological specimens disclosed herein can include one or more biological samples that can be a tissue sample or samples (e.g., any collection of cells) removed from a subject. The tissue sample can be a collection of interconnected cells that perform a similar function within an organism. A biological sample can also be any solid or fluid sample obtained from, excreted by, or secreted by any living organism, including, without limitation, single-celled organisms, such as bacteria, yeast, protozoans, and amoebas, multicellular organisms (e.g., plants or animals, including samples from a healthy or apparently healthy human subject or a human patient affected by a condition or disease to be diagnosed or investigated, such as cancer). In some embodiments, a biological sample is mountable on a microscope slide and includes, without limitation, a section of tissue, an organ, a tumor section, a smear, a frozen section, a cytology prep, or cell lines. An incisional biopsy, a core biopsy, an excisional biopsy, a needle aspiration biopsy, a core needle biopsy, a stereotactic biopsy, an open biopsy, or a surgical biopsy can be used to obtain the sample. 
       FIG. 3  is a block diagram of the system  100  in accordance with one embodiment of the disclosed technology. The system  100  can include an assay processing module  261  with a dispenser instrument  160  that includes one or more dispensing mechanisms  262  and the transporter apparatus  172 . The dispensing mechanisms  262  can include one or more actuators, plungers, positioners  266  (e.g., XYZ positioners) for moving actuators, or the like. 
     A reader in the form of a barcode reader  270  can acquire information from stainer units, slides, cartridges, containers or other items with labels or readable information. The information (e.g., consumable ID, tissue information, etc.) can be sent to a controller (e.g., controller  130  of  FIG. 1 ). The controller can determine a processing protocol based on the received information. Multiple readers can be used to increase throughput. The number, positions, and configurations of the readers can be selected based on target throughput, reading capabilities, or other operating parameters. 
     The assay processing module  261  can include support elements  289 . The support elements  289  can include one or more processors, sensors, controllers, waste containers, and housing components (e.g., frame, panels, etc.). Controllers can control processing environments, system components and/or communication and can include one or more displays for displaying user interfaces (UIs) or information, for example. Waste containers can store solid waste, such as used pipettor tips. The support elements  289  can include communication components (e.g., antennae, transmitters, ports, wireless modules, etc.), power supply conditioning/distribution components, or the like. The components and configuration of the support elements  289  can be selected based on, for example, whether the system  100  communicates with another system or network. 
     The assay processing module  261  can also include one or more valve control modules  290 , clamping modules  292 , consumable locator modules  294 , and/or temperature control modules  296 . The valve control modules  290  can include one or more sensors (e.g., pressure sensors, temperature sensors, etc.), valves (e.g., one-way valves, diaphragm or membrane valves, etc.), actuators (e.g., pushers for opening/closing diaphragm or membrane valves), and fluid lines, for example. The clamping module  292  can clamp onto the stainer unit. For example, the clamping module  292  can include a closure device (e.g., closure device  260  of  FIG. 2 ) configured to apply pressure to a cell (e.g., a reaction cell, a flow cell, etc.), slide, or the like. The consumable locator module  294  can physically locate and securely hold consumables. The temperature control module  296  can be part of a base (e.g., base  220  of  FIG. 2 ) and can include one or more thermal elements, insulators, controllers, or the like. Thermal elements can be conduction heaters/coolers, resistive heaters, and/or Peltier devices and can be capable of localized heating/cooling at the flow cell area, so the flow cell and its contents can be heated/cooled without substantially affecting the temperature of the stored reagents. 
       FIG. 4  is a top view of an automated slide processing system  201  configured for parallel processing of stainer units in accordance with an embodiment of the disclosed technology. The system  201  can include an array of processing zones or stations  291  (one identified), each capable of holding at least one stainer unit. Although the illustrated embodiment has eight stations  291 , system  201  can have any number of stations. Each processing station  291  can include a station  293  (two separate ones identified) configured to receive modules/cartridges, stainer units, or the like. Processing areas  295  surround respective stations  293 . The number of processing stations  291  can be selected based on the desired processing throughout. A waste reservoir or area  297  can include a container for collecting solid waste, liquid waste, or both. A supply station  286  can include a storage area (e.g., reagent cartridge rack area, a capsule storage area, etc.), coverslips, fluid containers, or the like. 
     In operation, stainer units can be manually or robotically loaded into the system  201  via a feed or input portal  246  (“input portal  246 ”). In some embodiments, an interrogation station  248  has a detector  250  positioned to analyze the slide, stainer units, or both. The detector  250  can include one or more readers, optical sensors, cameras, contact sensors, position sensors, or the like. A robotic transporter apparatus can retrieve stainer units from the station  248  and transport the retrieved stainer units to a desired zone or station. Each specimen-bearing slide can be processed based on one or more signals from the detector  250  according to, for example, one or more arbitrary user-defined sets of operations (e.g., a user-defined staining protocol), pre-defined sets of operations (e.g., preprogrammed protocol), or other processing instructions or routines. Processed stainer units can be parked at an output station  277 . The number of processing zones can be selected based on the desired processing throughout, the components and functionality of each processing zone can be selected based on the processing protocols to be performed, and the configuration of the system  100  can be selected based on the desired system footprint. 
     Sensors can be located at various locations throughout processing systems, including on transporters, within the processing zones, and incorporated into stainer units. In some embodiments, sensors (including, without limitation, strain gauges, accelerometers, contact sensors, optical sensors, or other sensing devices capable of sensing certain events) can be used to detect contact, collisions, impacts, or other events. The sensors can output one or more signals that are received by a controller, which can determine whether a given event requires user notification or other action. For example, if an unexpected position of a cover of a stainer unit is detected, the controller can alert a user to open an access door to visually inspect the stainer unit to determine, for example, whether the slide or cover is positioned properly. 
     The stainer units can include an integrated coverslip that covers the specimen to enable analysis without removing the slide from the stainer unit. In other embodiments, a slide can be removed from the stainer unit for manual or robotic coverslipping. In robotic coverslipping embodiments, a coverslipper can apply solvent to slides and can then place coverslips with pre-applied adhesive onto the slides. In one embodiment, the coverslipper is substantially as described in U.S. Patent Application Publication No. 2004/0092024A1 or U.S. Pat. No. 7,468,161, which are incorporated by reference herein in their entireties. The coverslippers described in U.S. Patent Application Publication No. 2004/0092024A1 or U.S. Pat. No. 7,468,161 and their operation can be implemented to enhance coverslip handling by, for example, detecting broken coverslips, facilitating single coverslip pickup, increasing coverslipper placement precision, and/or increasing system throughput. In some embodiments, the system  100  of  FIGS. 1 and 3  can have a coverslipper. Additional modules can be added to the processing systems disclosed herein to provide any number of functionalities for processing of specimens with minimal or no human intervention during normal operation. 
     The number of processing zones or stations can be selected based on the desired processing throughout, and the components and functionality of each processing zone or station can be selected based on the processing protocols to be performed. The automated specimen processing system  100  or  201  can have any shape, and the processing zones be arranged in any manner. Each processing zone can be configured to hold any number of stainer units, for example, 1 stainer unit, 2 or more stainer unit units, 3 or more stainer unit, or 5 or more stainer units, and the processing zones or stations can be arranged in a linear arrangement, circular arrangement, or other suitable arrangement. 
     II. Stainer Units/Slide Processing Modules 
       FIG. 5  is a perspective view of a stainer unit in the form of a slide processing module  108  in accordance with an embodiment of the disclosed technology. The slide processing module  108  can include a flow cell  210 , a dispenser unit  204 , and a reagent cartridge  316 . The flow cell  210  is configured to sealingly contact a microscope slide to provide a reaction chamber along a specimen-bearing slide surface. The dispenser unit  204  can function as a reagent dispenser and can include a capsule receiver  322  and a syringe or pump  324 , both fluidly coupled to the flow cell  210 . The reagent cartridge  316  holds reagent-filled capsules that can be sequentially fed to the capsule receiver  322 . An actuator  207  can be part of the slide processing module  108  or part of a dispenser mechanism (e.g., dispenser instrument  160 ) and can engage one or more capsules within the capsule receiver  322  to release reagent, which is then delivered to the flow cell  210 . 
     The slide processing module  108  can include a base  200  and a waste reservoir or container  380 . The base  200  can include a fluid circuit  382  fluidically coupling the dispenser unit  204  to the flow cell  210 . The fluid circuit  382  can include one or more passageways  392 , air-trap features  396 , valves  398 , and other fluidic elements. The base  200  can include another fluid circuit  397  that fluidly couples the flow cell  210  to the waste container  380 . Fresh reagent can flow along the passageway  392 , through the open valve  398 , and into the flow cell  210 , and waste liquid (e.g., reacted reagents) can flow along the waste passageway of the fluid circuit  397  and into the waste container  380 . The waste container  380  can include a container  384  and a removable or permanent cover  386 . 
       FIG. 6  is a perspective view of a slide processing module  108  with the flow cell  210  in an open configuration in accordance with an embodiment of the disclosed technology. A specimen-bearing microscope slide  388  is located at a set down or slide region slide-receiving  350  (“slide-receiving region  350 ”) in the base  200 . The flow cell  210  can include a cover  340  movable, as indicated by arrow  394 , from an open position ( FIG. 6 ) to a closed position ( FIG. 5 ). In some embodiments, a hinge  390  rotatably couples the cover  340  to the base  200  and can be a living hinge, a movable joint, a flexible element, or another feature that allows movement of the cover  340 . The hinge  390  can allow rotation of the cover  340  about a single axis of rotation to maintain alignment with the slide  388 . In other embodiments, the cover  340  may be separable from the base  200  to allow different covers to be used with the processing module  108 . 
     The cover  340  can include a sealing ring  391  and a tissue-receiving area  399  surrounded by the sealing ring  391 . When the cover  340  is in the closed position, the sealing ring  391  can sealingly contact an upwardly facing specimen-bearing surface  389  of the microscope slide  388  or the surface of the base  200  ( FIG. 8 ) to define a reaction chamber to prevent or limit air contact with the reagent, thereby reducing the likelihood of reagent degradation (e.g., oxidation) that would impair staining. To process a specimen on a downwardly facing specimen-bearing surface, the base  200  can have one or more sealing rings underneath the slide to define a reaction chamber under the slide. 
     The input fluid circuit  392  can include a fluid element  395  (illustrated in phantom line) that can be opened and closed to seal the flow cell  210  for high temperature processing, such as antigen/target retrieval. Example fluid elements  395  include membrane valves, diaphragm valves, butterfly valves, ball valves, check valves, or the like. An output fluid circuit  397  can include one or more fluid elements  399  that cooperates with the fluid element  395  to control fluid flow. The fluid circuits  392 ,  397  can include, without limitation, one or more pressure sensors, fluid passageways, channels (e.g., micro-channels), conduits, air-trap features, pressure regulators, or the like. 
     When the fluid elements  395 ,  399  are both closed to seal the reaction chamber, water-based reagents can be heated to temperatures higher than their normal boiling points (e.g., boiling points at atmospheric pressure) to provide enhanced target retrieval. This ensures that the reagent does not boil when it is at a temperature equal to or higher than about 100° C., about 105° C., about 110° C., about 115° C., or about 120° C. For example, the flow cell  210  can be closed and pressurized to raise the boiling point of the reagent (e.g., a reagent with a suitable target with associated marker) at least about 2%, about 5%, about 10%, about 20%, or about 30%. 
       FIG. 7  is a top view of the slide processing module  108  with the cover  340  in the closed position.  FIG. 8  is a cross-sectional view of the flow cell  210  taken along line  8 - 8  of  FIG. 9 . Referring now to  FIG. 7 , the reagent cartridge  316  can include a housing  326  and an array of reagent capsules  330  (one identified) each containing reagent. The reagent cartridge  316  sequentially feeds the capsules  330  to a capsule receiver  322  such that the capsules  330  are successively delivered to and burst within a chamber of the capsule receiver  322 . The capsules can be reagent-filled spherical or oblong vessels with a monolayer or multilayer shell comprising one or more materials suitable for contacting reagent therein. 
     The holding capacities of the capsules  330  can be substantially equal to each another to provide uniform dispensing volumes. In other embodiments, the capsules  330  can have varying volumes of reagents but may have similar shapes or sizes. For example, the shells can be partially filled or completely filled (if the shells have different wall thicknesses for providing the desired volume of reagent). In some embodiments, the capsules  330  hold a volume of reagent equal to or greater than at least about 0.5 mL, about 1 mL, about 2 mL, about 3 mL, about 4 mL, about 10 mL, about 20 mL, about 30 mL, about 40 mL, or about 50 mL. The contents, holding capacity, and shape/configuration of the capsules  330  can be selected based on the staining protocols to be performed. Table 1 below shows an example assay protocol and fluids, number of steps, volumes, and times (e.g., tissue exposure times). 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                 Fluid 
                 Number of Steps 
                 Vol (mL) 
                 Time (min) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                 CC2 
                 1 
                 0.3 
                 44 
               
               
                 AOS 
                 5 
                 1.3 
                 2.3 
               
               
                 ATF 
                 2 
                 0.6 
                 0.5 
               
               
                 RB 
                 11 
                 3.3 
                 2.8 
               
               
                 Enzyme Digestion 
                 1 
                 0.3 
                 20 
               
               
                 SSC 
                 1 
                 0.3 
                 0.3 
               
               
                 Denaturation 
                 1 
                 0.3 
                 24 
               
               
                 Hybridization 
                 1 
                 0.3 
                 364 
               
               
                 Stringency Wash 
                 1 
                 0.3 
                 36 
               
               
                 Silver 2nd Ab 
                 1 
                 0.3 
                 24 
               
               
                 Silver 3rd Ab 
                 1 
                 0.3 
                 36 
               
               
                 Silver A 
                 1 
                 0.1 
                 20 
               
               
                 Silver B 
                 1 
                 0.1 
                 0 
               
               
                 Silver C 
                 1 
                 0.1 
                 0 
               
               
                 Red Linker 
                 1 
                 0.3 
                 24 
               
               
                 Red Multimer 
                 1 
                 0.3 
                 24 
               
               
                 pH enhancer 
                 1 
                 0.1 
                 16 
               
               
                 napthol 
                 1 
                 0.1 
                 0 
               
               
                 Fast Red 
                 1 
                 0.2 
                 0 
               
               
                 Hematoxylin 
                 1 
                 0.3 
                 1 
               
               
                 Bluing 
                 1 
                 0.3 
                 0.2 
               
               
                   
               
            
           
         
       
     
     Multiple capsules  330  can be used to obtain the desired total reagent volume of a processing step. For example, three capsules  330 , each containing 0.1 mL of hematoxylin, can be burst to deliver 0.3 mL of hematoxylin to the flow cell  210 . The reagent cartridge  316  can hold a set of reagent capsules  330  in a predetermined order for a staining protocol selected for a particular specimen. If a preloaded cartridge does not include the desired capsules, capsules can be removed, replaced, and/or reordered according to the protocol to be performed. 
     The reagent cartridge  316  can include at least one biasing member  331  that urges one or more of the capsules  330  toward the capsule receiver  322 . The biasing member  331  can include one or more springs, such as helical springs, conical springs, or the like. In addition to and/or in lieu of biasing member(s), an instrument can include advancer (e.g., a push rod) that advances the capsules  330  toward the capsule receiver  322 . In gravity-feed embodiments, the reagent cartridge  316  can be at a substantially vertical orientation to hold the capsules  330  in a vertical stack, thereby reducing the complexity of the cartridge and/or instrument, but such reagent cartridge can further include one or more biasing members to enhance feeding of capsules. 
       FIG. 8  shows the reaction chamber  398  can have a holding capacity equal to or less than about 25 μL, 50 μL, 100 μL, or 200 μL. In some embodiments, the flow cell  210  can hold about 25 μL to about 100 μL, about 50 μL to about 100 μL, or other desired volumes. The sealing ring  391  can sealingly contact the upper surface  389  or base surface  409  (illustrated) to form a seal  410 . In some embodiments, the slide-receiving region  350  can include one or more heating elements  401  for generating thermal energy that is delivered uniformly or non-uniformly across the slide  388  via conduction to produce a substantially uniform or varying temperature profile along the specimen-bearing surface  389 . The heating elements  401  can provide active heating/cooling to achieve a set point temperature of about 20° C. to about 140° C. (+/−1° C.). In some embodiments, the base  200  can provide active heating/cooling to produce set point temperature along the surface  389  of about 20° C. to about 40° C., about 40° C. to about 60° C., about 60° C. to about 80° C., about 80° C. to about 100° C., about 100° C. to about 120° C., or about 100° C. to about 140° C. 
     The heating elements  401  can be spaced apart to heat substantially the entire mounting area of the slide to produce a substantially uniform temperature profile along the slide&#39;s width, length, or both. This ensures that any portion of a specimen contacting the mounting surface  389  is maintained at a generally uniform temperature for consistent processing. Even if specimens move slightly along the mounting surface  389 , the specimens can be consistently processed. In some embodiments, a substantially uniform temperature profile can be generated and may have less than selected temperature variation (e.g., a temperature variation of 1° C., 2° C., 5° C., or 10° C.) across the specimen-bearing portion (e.g., mounting area) of the specimen-bearing surface  389 . Alternatively, the base  200  can generate non-uniform temperature profiles to localize heating at the mounting area. 
     The sealing ring  391  can comprise one or more compressible materials (e.g., rubber, elastomer, silicone, or the like) capable of forming the seal  410 . The seal  410  can be a fluid-tight seal that prevents leaking of reagent and can be maintained when the pressure within the chamber  398  is at, above, or below a pressure of about 1 bar, 1.5 bar, 2 bar, 2.5 bar, 3 bar, 3.5 bar, or 4 bar, or other desired pressure suitable for pressurized staining. For example, a reagent within the chamber  398  can be at a pressure in a range of about 1 bar to about 4 bar, about 1.5 bar to about 3.5 bar, or the like. For a water boiling point of 140° C., the pressure can be about 3.6 bar (52 psi). The pressurized reagent can be heated to temperatures higher than the normal boiling temperature of reagent (e.g., when the reagent is at atmospheric pressure) to provide enhanced antigen/target retrieval. The chamber  398  can kept at a high enough pressure to inhibit or prevent boiling of the reagent when the reagent (e.g., a reagent comprising primarily water) is at a temperature equal to or higher than about 80° C. (e.g., taking into account higher altitude conditions), 90° C., 100° C., or 105° C. A clamping device or a user&#39;s hand can press the cover  340  against the slide  388  or base  200 , or both, with sufficient force to maintain the fluid-tight seal  410  based on the pressure level. 
     Longitudinally extending sides of the sealing ring  391  can sealingly contact flat specimen-bearing surface  389  and end sections of the sealing ring  391  can contact the base  200 . In some embodiments, the entire length of the sealing ring  391  can contact the specimen-bearing surface  389  to provide a continuous seal  410  surrounding the specimen  400  (shown in phantom line in  FIG. 7 ). The cover  340  can include one or more inlet ports for delivering fluid into the reaction chamber  398  located along the upwardly facing specimen-bearing surface  389 . The seal  410  can prevent surrounding air from entering the chamber  398  to limit or reduce degradation of the reagent. The configuration, mechanical properties (e.g., compressibility, resiliency, etc.), and composition of the sealing ring  391  can be selected based on, for example, desired sealing capabilities, reaction chamber dimensions, or the like. 
     With continued reference to  FIG. 8 , the flow cell  210  can include an inlet port  420  and an inlet sealing member  422 . The inlet sealing member  422  can have a one-piece or multi-piece construction and can be a compressible split ring, a gasket, or another sealing element configured to sealingly engage the cover  340 . To direct fluid toward the reaction chamber  298 , the sealing member  422  can include one or more openings, slits, thinned regions, or other flow-through features. 
     The flow cell  210  can include an outlet port  442  at a downstream end of the reaction chamber  398 . An outlet sealing member  450  can sealingly engage at least a portion of the cover  340  to inhibit or prevent reagent from escaping out of the flow cell  210  while waste reagent exits the reaction chamber  398 . The sealing member  450  can include one or more openings, slits, narrowed or thinned regions, other features for allowing waste reagent or other fluids to flow through the outlet port  442 . 
     In addition to and/or in lieu of the sealing members  422 ,  450 , the flow cell  210  can include one or more connections, such as male/female connectors. The position and number of inlet and outlet ports can be selected based on the desired flow through the chamber  398 . In some embodiments, a plurality of inlet ports  420  can be evenly or unevenly spaced along one side or end of the reaction chamber  398 . Additionally or alternatively, a plurality of evenly or unevenly spaced outlet ports  442  can be positioned at an opposing side or end of the reaction chamber  398 . 
     The cover  340  can have a surface  430  that can be generally parallel to the slide surface  402  to promote generally uniform laminar flow of reagent across the slide  388 . In other embodiments, the reaction chamber  398  can be configured to promote turbulent flow. The configuration, dimensions, and features of the reaction chamber  398  can be selected based on desired flow rates, flow characteristics, volume of reagent, and/or sealing capability. 
       FIG. 9  is a detailed cross-sectional view of the dispensing unit  204  in accordance with an embodiment of the disclosed technology.  FIG. 10  is a detailed cross-sectional view of the dispensing unit  204 .  FIG. 9  shows the capsule receiver  322  including a barrel  440  defining the chamber  444  such that the capsule receiver  322  and actuator  207  can cooperate to cause reagent to be released from any reagent capsule positioned in the chamber  444 . The dispenser  324  can be fluidically coupled, via passageway  482 , to the flow cell  210 , and if the dispenser  324  holds wash solution, it can hold a sufficient volume of wash solution to flush the reaction chamber. The dispenser  324  can hold other liquids. 
     The actuator  207  can be a plunger disposed within the barrel  440  and can be movable to move the capsule  330  against a puncturing element  450 . When the puncturing element  450  pierces a shell  460  of capsule  330 , reagent in a capture chamber  462  can flow through a passageway  470  through the puncturing element  450 .  FIG. 11  shows three emptied and collapsed shells  460  along the puncturing element  450 . In some embodiments, the dispensing unit  204  has an ejector mechanism for ejecting emptied shells  460 . A fluid passageway  472  can fluidly couple the dispensing unit  204  to the flow cell  210 . 
     Referring now to  FIG. 10 , the actuator  207  is located at a loading position for allowing the bottom-most capsule  330  to fall through an entrance  473  of the barrel  440  and into the chamber  444 . In a dispense mode, the actuator  207  can move toward the reagent capsule(s) located within the chamber  444  such that the actuator  207  causes the capsule(s) to release reagent. In reload mode, the actuator  207  can be located at a standby position, as shown in  FIG. 9 , to allow another reagent capsule to be delivered into the chamber. The actuator  207  can include one or more sealing members that slidably contact the wall of the barrel  440  while the actuator  207  is moved between a loading position ( FIG. 10 ) and a dispensing position (illustrated in phantom line in  FIG. 9 ). 
       FIG. 11  is a flow chart illustrating a method  900  for processing a specimen in accordance with an embodiment of the disclosed technology. In general, a stainer unit can be loaded with a specimen-bearing slide. The stainer unit can be delivered to an automated instrument, and the specimen is treated using one or more reagents carried by the stainer unit. After processing the specimen, the specimen-bearing slide can be removed from the stainer unit. Although method  900  is primarily discussed in connection with capsule-based processing module of  FIGS. 5-11 , the method can be performed using other stainer units. Details of the method  900  are discussed in detail below. 
     At block  910 , the processing module  108  can be loaded with a microscope slide placed at the set down area  350 . Specimens on the slide can have tissue fixed prior to placement in the processing module  108 . The cover  340  can be moved from the open position ( FIG. 6 ) to a closed position ( FIG. 5 ). 
     At block  920 , the processing module  108  can be delivered to the instrument. A user can input information into the instrument, and a controller can determine a program for operating the components based, at least in part, on the inputted information. The inputted information can include, without limitation, one or more staining protocols, tissue sample information, processing times, imaging protocols, or the like. The user can also select a stored program to perform a desired protocol. If the processing module and/or slide include a label (e.g., RFID tags, transponders, or the like) that contains information that can be acquired by, e.g., readers, scanners, or other devices, and the acquired information can be sent to the controller, which in turn determine an appropriate program. Different programs can be used to perform tissue conditioning, staining, target retrieval, IHC, ISH, etc. The programs can be calculated, determined, or selected based on information about the slide/specimen and/or the available reagents. For example, a program can be determined based on the available reagents carried by the processing module, composition of the specimen, tissue type, or the like. If the processing module cannot be used to process the specimen, the instrument can notify a user that another processing module should be used. 
     At block  930 , the instrument can treat the specimen using reagents from the processing module. The holding capacity of the reagent capsules can be in a range of about 20 μl to about 100 μl, about 100 μl to about 200 μl, about 1 microliters to about 5 microliters, 5 microliters to about 50 microliters, about 25 microliters to about 75 microliters, but more typically, the capsules will have a holding capacity in the equal to or less than about 25 μL, about 50 μL, about 100 μL, about 150 μL, or about 200 μL. In some embodiments, the capsules can hold about 25 μL to about 100 μL, about 50 μL to about 100 μL, about 75 μL to about 120 μL or other desired volumes. If the processing module is configured for receiving reagents from pipettes, the pipettes can have similar holding capacities. 
     The dispenser apparatus  160  ( FIG. 2 ) can operate to cause reagent to be released sequentially from the capsules. The released reagent can flow into the flow cell  210  to fill the reaction chamber  398  ( FIG. 8 ). The closed flow cell can prevent evaporative losses to avoid using excessive amounts of reagent. The reagent can be replenished with fresh reagent any number of times to achieve desired staining. For example, the controller  130  ( FIG. 1 ) can instruct the dispenser apparatus  160  to provide supplemental reagent at a desired rate (e.g., a fixed rate or a variable rate) based on the degradation or oxidation rates of the liquid. 
     In some protocols, a series of liquids can include, for example, a deparaffinizing liquid, a conditioning liquid, a staining reagent, a stain-differentiating reagent, a stain-setting reagent, a counterstaining reagent, a washing liquid, and a coverslipping liquid. During deparaffinizing, a paraffin composition in which the specimen is embedded can be at least partially removed to prepare the specimen for further processing. The system  201  of  FIG. 4  can process slides in parallel. In at least some cases, deparaffinizing includes iterations (e.g., 4, 5, 6, 7, 8, or another suitable number of iterations) of dispensing a deparaffinizing liquid onto slides respectively carrying the specimens, allowing the dispensed deparaffinizing liquid to remain in contact with a paraffin composition in which the specimens are embedded for a suitable period of time so as to solubilize a portion of the paraffin composition, and then removing the dispensed deparaffinizing liquid along with a solubilized portion of the paraffin composition. 
     After deparaffinizing and conditioning, staining, target retrieval, IHC, ISH, or other processes can be performed on the conditioned specimen. Optional washing can include iterations (e.g., 2, 3, or another suitable number of iterations) of dispensing a washing liquid onto a slide, allowing the dispensed washing liquid to remain in contact with the specimen for a suitable period of time so as to wholly or incrementally wash the specimens (e.g., while the washing liquid is in the form of a puddle having a shape maintained at least partially by surface tension), and then removing the dispensed washing liquid. The washing liquid can flush out the deparaffinizing and solutions. The time during which the dispensed washing liquid is in contact with the specimen can be, for example, a time within a range from 5 seconds to 45 seconds, from 20 seconds to 1 minute, or the like. When used in temperature-controlled flow cells configured in accordance with at least some embodiments of the present technology, incubation temperatures can be used alone or in conjunction with incubation time to control processing. 
     The seal  410  ( FIGS. 7 and 8 ) can be a fluid-tight seal that prevents leaking of reagent and can be maintained when the pressure within the chamber  398  ( FIG. 8 ) is at or above a threshold suitable for pressurized staining. The pressurized reagent can be heated to temperatures higher than the normal boiling temperature of reagent (e.g., when the reagent is at atmospheric pressure) to provide enhanced antigen retrieval. The chamber  398  can kept at a high enough pressure to inhibit or prevent boiling of the reagent when the reagent (e.g., a reagent comprising primarily water) is at a temperature equal to or higher than about 100° C. or 105° C. For example, the chamber  380  can be sealed by closing the valves  353 ,  355 , and the seal  370 , as well as any other seals of the flow cell, can be selected to increase the boiling points of reagents or buffers at least about 5%, 10%, 15%, 20%, or 25%. Enhanced staining can be achieved in very short times with such an arrangement. A clamping device or a user&#39;s hand can press the cover  340  against the slide  388  with sufficient force to maintain the fluid-tight seal  410 . In some embodiments, the seal  410  prevents surrounding air from entering the chamber  398  to limit or reduce degradation of the reagent. The configuration, mechanical properties (e.g., compressibility), and composition of the sealing gasket  392  can be selected based on, for example, desired sealing capabilities, reaction chamber dimensions, or the like. 
     The specimen can be dehydrated and a coverslip can be applied. Coverslipping liquids can be applied directly to the microscope slide after opening the cover. A coverslipping liquid selected or formulated in accordance with a particular embodiment of the present technology includes about 100% d-limonene with a suitable preservative, such as 500 parts per million butylated hydroxytoluene. After applying the coverslipping liquid, the system can then apply coverslips. 
     At block  940 , the processing module  108  can be removed from staining instrument and opened to remove the processed slide. The specimen can be microscopically analyzed. The waste materials (e.g., reacted reagent) can be contained in a waste container of the processing module throughout slide removal and disposal. In some procedures, coverslipping is performed after removing the slide from the processing module. 
     At block  950 , the processing module itself or its disposable components can be discarded. As used herein, the term “disposable” when applied to a system or component (or combination of components), such as a stainer unit or processing module, is a broad term and means, without limitation, that the component in question is used a finite number of times and then discarded. Some disposable components are used only once and then discarded. Other disposable components are used more than once and then discarded. For example, a disposable waste container can be used to collect waste generated by a single assay and is then discarded whereas a base of a module can be used multiple times. 
     Although various operations are presented in a sequence(s), it should be understood that the various operations discussed in connection with method  900  may be performed in orders other than those that are illustrated, or may be performed concurrently. Examples of such alternate orderings includes interrupted, reordered, supplemental, simultaneous, reverse, or other variant orderings, unless context dictates otherwise. For example, the specimens can be pretreated, either manually or robotically, with conditioners prior to delivery to the instrument at block  920 . In some embodiments, the flow cell can be opened to access the slide for coverslipping. In one embodiment, a coverslipper as substantially as described in U.S. Patent Application Publication No. 2004/0092024A1 or U.S. Pat. No. 7,468,161, which are incorporated by reference herein in their entireties, can be integrated the systems disclosed herein. After opening a cover, the automated coverslipper can apply the coverslip to the uncovered slide. The coverslippers described in U.S. Patent Application Publication No. 2004/0092024A1 or U.S. Pat. No. 7,468,161 and their operation can be implemented to enhance coverslip handling by, for example, detecting broken coverslips, facilitating single coverslip pickup, increasing coverslipper placement precision, and/or increasing system throughput. 
     The various embodiments described above can be combined to provide further embodiments. The embodiments, features, systems, devices, materials, methods, and techniques described herein may, in some embodiments, be similar to any one or more of the embodiments, features, systems, devices, reagents, processing steps, materials, methods, and techniques described in U.S. patent application Ser. No. 11/187,183; U.S. patent application Ser. No. 13/509,785; U.S. patent application Ser. No. 13/509,785; U.S. patent application Ser. No. 13/157,231; U.S. Pat. Nos. 7,468,161; 9,618,430; and 8,790,596; PCT Application No. PCT/EP2019/068814; U.S. Provisional Application No. 62/698,820; and International App. No. PCT/US2010/056752, all of which are incorporated by reference in their entireties. In addition, the embodiments, features, systems, devices, materials, methods, and techniques described herein may, in certain embodiments, be applied to or used in connection with any one or more of the embodiments, features, systems, devices, materials, methods, and techniques disclosed in the above-mentioned U.S. patent application Ser. No. 11/187,183; U.S. patent application Ser. No. 13/509,785; U.S. patent application Ser. No. 13/509,785; U.S. patent application Ser. No. 13/157,231; U.S. Pat. Nos. 7,468,161; 9,618,430; and 8,790,596; and International App. No. PCT/US2010/056752. Aspects of the disclosed embodiments can be modified, if necessary, to employ concepts of the various patents, applications, and publications to provide yet further embodiments. All applications listed above are incorporated herein by reference in their entireties. 
     From the foregoing, it will be appreciated that specific embodiments of the invention have been described herein for purposes of illustration, but well-known structures and functions have not been shown or described in detail to avoid unnecessarily obscuring the description of at least some embodiments of the invention. The systems, apparatuses, and components described herein can perform a wide range of processes for preparing biological specimens for analysis. The scheduling and methods disclosed herein can be used with different types of specimen processing systems with apparatuses configured to deliver liquid into reaction chamber. In other embodiments, one, multiple, or all of the steps can be performed manually. In some embodiments, a combination of manual steps and automated steps can be performed. Where the context permits, singular or plural terms may also include the plural or singular term, respectively. Unless the word “or” is associated with an express clause indicating that the word should be limited to mean only a single item exclusive from the other items in reference to a list of two or more items, then the use of “or” in such a list shall be interpreted as including (a) any single item in the list, (b) all of the items in the list, or (c) any combination of the items in the list. The singular forms “a,” “an,” and “the” include plural referents unless the context clearly indicates otherwise. Thus, for example, reference to “a specimen” refers to one or more specimens, such as two or more specimens, three or more specimens, or four or more specimens. 
     The various embodiments described above can be combined to provide further embodiments. The embodiments, features, systems, devices, materials, methods, and techniques described herein may, in certain embodiments, be applied to or used in connection with any one or more of the embodiments, features, systems, devices, materials, methods, and techniques disclosed in the above-mentioned patents and applications. Aspects of the disclosed embodiments can be modified, if necessary, to employ concepts of the various above-mentioned patents, applications, and publications to provide yet further embodiments.