Automated sample processing apparatus and a method of automated treating of samples and use of such apparatus
An automated staining apparatus and a method for treating samples arranged on a carrier is disclosed, in which portions of two or more selected reagents from a first station containing the reagents are collected individually by a robot arm handling a probe and dispensed in a mixing station of the apparatus. After mixing the reagents in the mixing station, e.g. by shaking or rotating the mixing cup containing the reagents, the reagent mixture is applied to selected samples by the robot arm and a probe.
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 This application claims the benefit of U.S. Provisional Application No. 60/435,601, filed Dec. 20, 2002, hereby incorporated by reference.FIELD OF INVENTION
 This application relates to the field of sample processing systems and methods of processing samples. The present invention may be directed to the automated processing, treatment, or even staining of samples arranged on carriers, such as slides, and in some embodiments, directed to the continuous or batch processing of samples and carriers, as well as washing elements of a sampling system. Embodiments may further relate to control systems for sample processing and data acquisition, data maintenance, and data retrieval for sample processing. Applications to which the present invention may especially relate include immunohistochemistry, in-situ hybridization, fluorescent in-situ hybridization, special staining, and cytology, as well as potentially other chemical and biological applications.
 More specifically the present invention relates to an automated sample processing apparatus for treating samples arranged on carrier means, such as microscope slides or sample tubes, located at defined positions close to or in the apparatus by aspirating a portion of selected reagent from a station containing a plurality of reagents and thereafter dispense the reagent to a sample, e.g. a tissue, organic cells, bacteria etc., arranged on the carrier means. The invention facilitates that two or more reagents are mixed and the mixture applied to a sample.
 The invention also relates to a method of automated treating of samples by mixing reagents and dispensing the mixture to the sample.
 A sample is in this application to be understood as a biological sample such as histological samples, e.g. tissue and cell specimens, including cell lines, proteins and synthetic peptides, tissues, cell preparations, blood, bodily fluids, bone marrow, cytology specimens, blood smears, thin-layer preparations, and micro arrays, and specifically biological samples on microscope slides.BACKGROUND OF INVENTION
 Sample processing in immunohistochemical (IHC) applications and in other chemical and biological analyses may require one or a number of various processing sequences or protocols as part of an analysis of one or more samples. The sample processing sequences or protocols may be defined by the individual or organization requesting an analysis, such as a pathologist or histologist of a hospital, and may be further defined by the dictates of a particular analysis to be performed.
 In preparation for sample analysis, a biological sample may be acquired by known sample acquisition techniques and may comprise, for example in IHC applications, tissues generally or even in some applications one or a plurality of isolated cells, such as in microarray samples, and may be presented on a sample carrier such as a microscope slide. Furthermore, the sample may be presented on the carrier variously and potentially in some form of preservation. As one example, a sample such as a layer or slice of skin may be preserved in formaldehyde and presented on a carrier with one or more paraffin or other chemical layers infiltrating the sample.
 Immunologic and histological applications, for example, may require processing sequences or protocols that comprise steps such as deparaffinization, target retrieval, and staining, especially for in-situ hybridization (ISH) techniques. Previously, in some applications, these steps may have been performed manually, potentially creating a time-intensive protocol and necessitating personnel to be actively involved in the sample processing. Attempts have been made to automate sample processing to address the need for expedient sample processing and a less manually burdensome operation. However, such previous efforts may have not fully addressed the needs for an automated sample processing system. Previous efforts to automate sample processing may be deficient in several aspects that prevent more robust automated sample processing, such as: the lack of sufficient computer control and monitoring of sample processing; the lack of information sharing for processing protocol and processing status, especially for individual samples; the lack of diagnostic capabilities; and the lack of real-time or adaptive capabilities for multiple sample batch processing.
 Past efforts at automated sample processing for samples presented on carriers such as slides, such as U.S. Pat. No. 6,352,861 to Ventana Medical Systems, Inc. and U.S. Pat. No. 5,839,091 to LabVision Corporation, have not afforded the various advantages and other
 Sample processing apparatuses for staining and treating samples by means of probes normally comprises a first station for containing one or more reagent vials; a second station for mounting slides, a probe arranged to aspirate a portion of reagent from a selected reagent vial and dispensing the reagent to a slide on which the sample is arranged and a drive means for moving the probe between the various stations.
 U.S. Pat. No. 5,948,359 discloses an apparatus of the above mentioned type, wherein the first station comprises a vial holder for holding 40 or more vials in order to provide a wide range of different reagents adapted for different staining purposes, and thereby the possibility of automatically staining a large number of slides requiring different staining processes. In practise it is very important that the apparatus facilitates that many different staining processes can be performed at the same time in the apparatus, because this avoids the necessity of batching samples requiring the same procedure or other treatment with reagents, and processing each batch individually.
 U.S. Pat. No. 5,723,092 discloses a sample dilution well for an immunoassay analyser in which a sample and a diluent is mixed by rotating the sample dilution well. Samples such as plasma or urine are loaded into the immunoassay analyser in a number of sample containing tubes, and a probe is arranged for collecting a portion of the sample in a selected sample carrying tube and transferring the sample to the dilution well, adding a portion of diluent, such as water to the sample portion and mixing the two by rotating the dilution well, after which a portion of the diluted sample is aspirated from the dilution well for examination.
 The mixing of reagents is known from U.S. Pat. No. 5,425,918 disclosing a staining apparatus for treating samples arranged on carrier means, comprising a vial station for containing at least two reagent vials, a carrier means station arranged for intermediate storage of a plurality of carrier means, probe drive means arranged for moving a probe, wherein the probe drive means is arranged to aspirate a portion of reagent from a selected reagent vial of the vial station by means of a probe and to apply reagent to a selected carrier means of the carrier means station. In this document it is suggested how to solved the problem regarding agents requiring mixing just prior to use due to short active lifetimes after mixing. The agents may be mixed by use of the probe and probe drive means drawing up one agent from its storage vial and dispensing it into the storage vial of the second agent. The mixed solution is then drawn up and dispensed onto the slides.
 Mixing wells for mixing samples and diluents are also disclosed by U.S. Pat. No. 4,323,537, in which an analysis system is described having mixing cuvettes for mixing sample and diluents by rotation and a displaceable probe for collecting the raw sample from a sample container and deliver it to the mixing cuvette, and for collecting the diluted sample from the cuvette after mixing and deliver it to a plurality of analysis stations for further, automated analysis.
 Methods for mixing reagents and liquids are well known—but several aspects are important in the context of IHC and ISH instruments wherein the mixing in some processes can be cumbersome.
 The staining procedure is laborious and uses many different reagents. The staining protocol may include the following steps: deparaffination, washing, antigen retrieval, endogenous biotin or enzyme blocking, incubation with immunological reagents, molecular probes, secondary visualization reagents and various chromogen reagents, washing steps and counterstaining.
 An on-board mixing device should be able to mix a multiple of reagents and mixtures. Non-limiting examples include:
 Dilution of chromogens concentrates, mixing and dilution of two, three or four component enzyme chromogen reagents, dilution of buffer concentrates, dilution of immunological reagents with dilution buffer, dilution of visualization reagents with dilution buffers, mixing several visualization reagents with dilution buffer or dilution of enzyme blocking reagents, dilution of biotin blocking reagents or mixing and dilution of counterstaining reagents.
 During the mixing several problems may arise. Some problems arise due to the complex use of reagents in the staining procedure. Below a few non-limiting examples are listed in more detail:
 The chromogen reagents (e.g. DAB, AEC, fast red etc) often comes as concentrated reagents in organic or high viscosity solutions and needs to be diluted prior to being applied to the sample.
 Chromogens like the Fast Red alkaline phosphatase chromogen are made ready for use by mixing and dilution of two or three reagents, which are very different in nature with regard to salt content, viscosity and density. Furthermore, the resulting mixtures are unstable over time and need to be used within a short time.
 Some chromogens suitable for e.g. horseradish peroxidase, like DAB and AEC, are easily oxidized when exposed to air during e.g. vigorous mixing or dilution.
 The enzyme chromogens and counterstain reagents like e.g. hematoxylin, are semi oxidized and can contain precipitates and solids. By further oxidation or slight change in pH, the reagents can further precipitate.
 Antibody and enzyme containing reagents often contain stabilizing proteins and or detergents, which causes the solution to foam when being shaken or stirred. Many proteins cannot easily tolerate to be exposed to the hydrophobic air in foam.
 Wash buffers can contain detergents, which can foam when shaken or stirred. The foam can spread to other compartments of the instrument in an unwanted and unpredictable way.
 Mixing of some reagents like e.g. the HRP chromogens and peroxide reagents can result in the formation of small bobbles. These can generate foam or bubbling on the surface of the mixture.
 Spill over/carry over must be avoided. The staining process is characterized by using many, complex and very different reagents and buffers and in many different dilution ratios and mixtures. Some of the reagents or buffers are incompatible with each other's. In the event of cross contamination due to e.g. carry over, the reagents may be ruined within seconds or solids can precipitate, making the staining unsuccessful. For example, enzyme containing reagents can not be mixed with the corresponding chromogens, or high salt concentrates may not be mixed with e.g. proteins containing mixtures, or organic solvents can not be mixed with protein containing mixtures, or highly pH buffered wash buffers can not be mixed with low buffered mixtures without significantly altering the properties of the reagents. Accordingly the cleansing and washing of the mixing device need to be very efficient.
 As the procedures are very complex, and the instrument uses many different protocols, one cannot predict the result of reagent carry-over or unplanned mixing of reagents. Consequently, the mixing device should ideally be very efficient and be designed for a variety of reagent mixing protocols and sequences.
 Build-up of small fouling layers on the surfaces will fast cause problems, as the typical staining protocol calls for many mixing and dilution steps. Consequently, the mixing device should have a minimum of surface area and very smooth surfaces.
 Furthermore, the mixing device should ideally be able to mix very different volumes of reagents in both small and large volumes ratios. In other words, the degree of dilution and mixing ratios of reagents may vary from small to high ratios.
 In summary, the mixing device should ideally allow:
 Mixing of small and large volumes
 Mixing reagents with different viscosities and densities
 Mixing of immiscible or nearly immiscible reagents
 No fouling of mixing rods or similar due to precipitated material
 Allow easy escape of formed gasses during mixing
 Prevent foaming of e.g. detergent or protein containing reagents
 Low build-up of debris or fouling on the device surfaces
 Easy emptying and washing—regardless of volumes
 Very low reagent carry-over
 No present mixing system truly fulfils the above-mentioned properties. On the slide mixing does not allow for very large ratios of dilution. Nor does it allow for efficient mixing of reagents with very different densities or viscosity.
 The object of the present invention is to improve the known apparatuses for sample processing as well as the method for automatic sample processing by facilitating a wider range of available processes of treatment, so as to increase the number of different staining and/or treatment processes that may be performed automatically, alternatively or additionally to provide an increased quality of some specific staining processes.SUMMARY OF INVENTION
 By providing a staining apparatus having an automated mixer integrated therein, staining or treatment processes requiring a mixture of unmixable reagents, such as a water based and an oil based reagent, or insoluble reagents, can be performed automatically instead of requiring human interaction or manual performance of some process steps in a much more automated process, and the quality of the staining process may be improved as a desired degree of mixing of reagents may be provided or an optimal application time window for a deteriorating mixture may be reached.
 This is achieved by the sample processing apparatus according to the present invention, comprising a reagent mixer having
 a mixing cup for receiving or more broadly adapted to receive two or more reagents and mixing means for mixing or more broadly a mix element adapted to mix the reagents in the mixing cup, and
 means for dispensing the reagent mixture from the mixing cup to a selected carrier means.
 An apparatus according to the invention may comprise an automated sample processing system comprising a plurality of drawers, a plurality of sample carrier retainment assemblies each removably configured with one of the drawers, and an adaptive sample processing control system to which the drawers and the sample carrier retainment assemblies are responsive. The sample carrier retainment assemblies may comprise slide retainment assembly and may be removably configured with the drawers to provide sample processing with the drawers of the system. The adaptive sample processing control system may automate the sample processing system such that one or more batches of samples may be processed according to one or more protocols, potentially indicated by information on the slides that may be automatically identified by the adaptive sample processing control system. Sample processing may comprise one or more sampling protocols and steps, such as deparaffinization, target retrieval, and staining.
 The term staining is used for the end product of the process, by which certain parts of the sample may be stained, i.e. have obtain a different colour, either in the optic range or in another electromagnetic range, such as ultra violet, or the staining may be an detectable, preferably automatically detectable, change in properties, such as fluorescent properties, magnetic properties, electrical properties or radioactive properties. To obtain the staining, the sample normally have to undergo a series of treatment steps, such as—but not limited to—washing, binding of reagents to the specific parts of the sample, activation of the reagents, etc. and each treatment step may include a plurality of individual treatments.
 In some staining processes, it is required for one or more treatments to use a mixture of reagents prepared from two or more separate reagents which may be somewhat incompatible e.g. unmixable, such as a water based and an oil based reagent, or insoluble, and therefore requires that the two or more reagents are manually prepared and introduced into a reagent vial shortly before starting the staining process in order to obtain the best possible staining result for the selected examination purposes. For other processes, different staining process steps require a mixture of the same two reagents but in different dissolution ratios. Some process step may require a mixture of two or more reagents that, when mixed, becomes unstable, e.g. has a limited time window of usability because internal chemical processes deteriorates the mixture. By providing a sample processing apparatus having an automated mixer integrated therein, these types of staining processes can be performed automatically instead of requiring human interaction or manual performance of some process steps, thereby achieving a much more automated process, and the quality of the staining process may be improved as a desired degree of mixing of reagents may be provided as well as an optimal application time window for a deteriorating mixture may be reached.
 Thus, the present invention relates to a sample processing apparatus for treating samples arranged on carrier means or carrier, comprising
 a vial station for containing at least two reagent vials, a carrier means station or more broadly a carrier station arranged for intermediate storage of a plurality of carrier means or carriers,
 probe drive means, or more broadly a probe drive arranged for moving or more broadly adapted to move a probe,
 wherein the probe drive means is arranged to aspirate a portion of reagent from a selected reagent vial of the vial station by means of or even with a probe and to apply reagent to a selected carrier means of the carrier means station,
 wherein the apparatus comprises a mixing station with a reagent mixer having a mixing cup for receiving or adapted to receive two or more reagents and mixing
 means for mixing or more broadly a mixer element adapted to mix the reagents in the mixing cup, and
 means for dispensing the reagent mixture from the mixing cup to a selected carrier means of the carrier means station.
 The vial station is a collection of a plurality of vials, at least two, but often 20-60 vials or more, which may or may not be physically arranged in close proximity to each other. The term station does not indicate that the vials must be located within one, confined area; rather it indicates the existence of a plurality of vials. The probe drive means or even probe drive may be a robot arm with two or three degrees of freedom, such as an articulated arm or one track or a set of perpendicular tracks along which a probe retainer of the probe drive means may be displaced, wherein the probe retainer may be moved in a direction normal to the track or tracks. The skilled person may readily design other types of probe drive means, e.g. combinations of the above described. The carrier means or even carrier may be provided to the apparatus in a two-dimensional array, e.g. constituted by individual rows of carrier means as discussed in the example below, or the carrier means may be provided in any manner known in the art, e.g. arranged in a carrousel or as a row of carrier means. The carrier means may also be arranged movably with respect to the probe drive means, such as in an endless row that is advanced automatically past the operating area of the probe drive means or as a two-dimensional array that may be moved in a direction perpendicular to a travel direction of the probe drive means, so that the probe may reach any carrier means by the combined movement of the probe and the array.
 The carrier means are preferably arranged in groups or series on trays or the like, so that a plurality of carrier means may be removed from or inserted into the apparatus simultaneously, and the apparatus preferably also comprises means for performing the intermediate storage of the carrier means with samples thereon and the removal of the carrier means from the apparatus automatically.
 The operation of the sample processing apparatus will generally be controlled by means of control means, typically a computer having a central processing unit and one or more memory unit associated therewith, means for controlling or more broadly a control element the various operations of the apparatus by controlling step motors, solenoids, valves and/or other drive or control parts of the apparatus. The control means may have one or more data communication ports for enabling data communication with external computers by wire or wireless. The control means does not have to be physically arranged within the apparatus itself but may be a computer external to the sample processing apparatus and connected to the apparatus via a data transmission port thereof.
 It is advantageous that the probe drive means is arranged to apply the reagent mixture from the mixing cup to selected carrier means. The mixed reagents from the mixing cup may be applied to the samples by separate means, such as a separate probe and probe drive means. In an alternative embodiment the carrier with the sample in question may be moved to a location at an outlet from the mixing cup. However it is presently preferred to use the probe drive means for the task.
 The mixing cup may receive the two or more reagents to be mixed from a separate set of vials or other reagent sources, but it is for rationalisation of the apparatus preferable that at least some of the reagents to be mixed may come from the same vials as are used for containing reagents to be applied to the samples. In a preferred embodiment, the probe drive means is therefore arranged to aspirate portions of reagents from at least two selected reagent vials of the vial station and apply said portions of reagents to the mixing cup.
 The mixing means or more broady a mix element of the reagent mixer may advantageously be constituted by cup drive means or more broadly a cup drive arranged for cyclic movement of the mixing cup, e.g. shaking or rotation in a horizontal or a vertical plane, so as to mix reagents contained in the mixing cup. The mixing of the reagent may be further improved by arranging mixing elements, such as blades or edges within the cup and stationary with respect to the cup. Other known mixer types may instead be preferred, such as shaft-driven impellers or magnetically driven impellers.
 The cyclic movement is preferably a rotation of the mixing cup, advantageously about a substantially vertical axis. The rotation is in a preferred embodiment an intermittent rotation in a clockwise and in an anticlockwise direction. Preferably the rotation speed may be varied through control means acting upon a driving motor in such manner that the fluid content inside the mixing cup is agitated, but at so low speed that substantially all reagents remain in the mixer cup. Preferably the speed may be controlled depending on the type of reagent in the mixer cup. Preferably the speed is controlled according to the processing protocol controlling the processing of the sample(s) to be processed in the apparatus. Preferably the rotation pattern (speed and direction) is controlled by controlling means or more broadly a control element, such as a computer, according to the sample processing protocol, thereby optimising the quality the mixing in the mixer cup in respect to the reagents present in the mixer cup. For the sake of good order, by sample processing protocol is meant a sequence of processing steps defined for the actual sample treated in the sample processing apparatus.
 In order to provide an efficient and fully automated cleansing of the mixing cup when changing from one reagent mixture to the next, it is advantageous that the mixing cup has inner walls extending upwardly and outwardly from a bottom part of the mixing cup, and the cup drive means is capable of rotating the mixing cup at an angular speed sufficient to fling all reagents contained therein out of the mixing cup. Preferably the inner walls are smooth and may terminate in an upper rim at the widest inner diameter of the mixing cup, in which case the high-speed rotation, preferably about a symmetry axis of the cup, will cause the waste reagent or cleansing liquid to be flung out over this upper rim. In an alternative embodiment of the mixer, the inner walls of the cup extend upwards and inwardly above the level of the widest inner diameter, at which one or more exit openings are provided in the inner wall as outlets for the waste reagent or the cleansing liquid. The top may be open for the probe to enter the mixing cup, or it may be closed to facilitate that the cyclic movement of the mixing cup for mixing the reagents may have a vertical component. The probe may in this case enter the mixing cup through one of the exit openings.
 To collect the waste reagent or the cleansing liquid, it is preferred that the reagent mixer comprises a waste reagent collecting chamber having a sidewall part laterally surrounding the mixing cup and arranged to collect reagents flung out of the mixing cup by rotation of the cup.
 In a further preferred embodiment, the reagent mixer further comprises a mixing cup holder for receiving and supporting the mixing cup in a releasable manner, so that different mixing cups may be used for different reagent mixtures.
 In yet further preferred embodiment, replacing means are provided for replacing the probe that is moved by the probe drive means with another probe, so as to avoid contamination of the reagents in the various reagent vials by the use of more than one probe. This may be combined with a probe washing station, in which one probe is washed after it has been replaced at the probe drive means so that it is clean and ready for repeated use without risking contamination of the content of the reagent vials.
 The present invention also relates to a method of fully automated treating of samples arranged on carrier means by means of a sample processing apparatus controlled by means of a control means, wherein the method comprises the steps of:
 arranging a plurality of carrier means intermediately in a carrier means station, each carrier means having a sample arranged thereon,
 dispensing a portion of a first reagent selected from a plurality of reagents to a mixing cup,
 dispensing a portion of a second reagent selected from a plurality of reagents to the mixing cup,
 mixing the reagents in the mixing cup by means of mixing means,
 moving a probe to the mixing cup by means of a probe drive means,
 aspirating a portion of the mixed reagents from the mixing cup by means of the probe,
 moving the probe to a selected one of said carrier means, and
 dispensing the mixed reagents to the selected carrier means,
 so as to perform a treatment of the sample arranged on the selected carrier means.
 In a preferred embodiment, the steps of dispensing portions of the first and the second reagents comprises the steps of
 moving a probe to a first, selected reagent vial by means of the probe drive means or even with a probe drive,
 aspirating a portion of the first reagent from the first reagent vial by means of the probe or even with a probe,
 moving the probe to the mixing cup by means of the probe drive means, dispensing the portion of the first reagent to the mixing cup,
 moving a probe to a second, selected reagent vial by means of the probe drive means or even with a probe drive,
 aspirating a portion of the second reagent from the second reagent vial by means of the probe or even with a probe,
 moving the probe to the mixing cup by means of the probe drive means or even with a probe drive, and
 dispensing the portion of the second reagent to the mixing cup.
 In a further preferred embodiment of the present invention, the method further comprises the step of replacing the probe arranged with the probe drive means with another probe between handling two different reagents or between handling a reagent and a reagent mixture.
 The present invention further relates to the use of an apparatus of the present invention as described above for exercising the method of the present invention. More specifically the invention relates to the use of the apparatus for IHC and ISH and sample processing of the type using special stains as well as batch-mode sample processing.
 Support should be understood to exist for the following aspect and embodiment of the invention: use of an apparatus according to any of the apparatus claims for exercising the method according to any of the method claims for immunohistochemistry and in-situ hybridization. Also support should be understood to exist for use of an apparatus according any of the apparatus claims for exercising the method according to any of the method for batch-mode sample processing.BRIEF DESCRIPTION OF THE FIGURES
 The invention will now be explained in further detail with reference to the enclosed drawing, wherein
 FIG. 1 is a perspective view of a sample processing apparatus according to the invention,
 FIG. 2 is a plan view of a sample processing apparatus according to the invention,
 FIG. 3 is a perspective view of a detail of the sample processing apparatus according to FIG. 2,
 FIG. 4 is a perspective view of a reagent mixer according to the invention, and
 FIG. 5 is a vertical cross-section of the reagent mixer according to FIG. 4.DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS OF THE INVENTION
 As mentioned earlier, the present invention includes a variety of aspects, which may be combined in different ways. The following descriptions are provided to list elements and describe some of the embodiments of the present invention. These elements are listed with initial embodiments, however it should be understood that they may be combined in any manner and in any number to create additional embodiments. The variously described examples and preferred embodiments should not be construed to limit the present invention to only the explicitly described systems, techniques, and applications. Further, this description should further be understood to support and encompass descriptions and claims of all the various embodiments, systems, techniques, methods, devices, and applications with any number of the disclosed elements, with each element alone, and also with any and all various permutations and combinations of all elements in this or any subsequent application.
 The embodiment shown in the figures and described in details below is only an example of an apparatus in accordance with the present invention and is not limiting the wider scope of the invention as described in the enclosed claims.
 FIG. 1 shows one schematic embodiment of a sample processing system 1 in accordance with the present invention. Cabinet sections form outer portions of the system and serve to address general structural considerations of the system (a top cabinet section is not shown in FIG. 1). The sample processing system may comprise a plurality of drawers used for the handling and processing of samples and sample carriers such as slides, potentially microscope slides. Other sample carriers may be accommodated consistent with the present invention. Each drawer may be configured to accommodate sample carrier retainment assemblies, such as slide retainment assemblies, carrier racks, modules, or magazines.
 One embodiment of a sample carrier retainment assembly may comprise a slide retainment assembly. The slide retainment assembly may comprise a slide rack, module, or magazines. Slide retainment assembly is configured to accommodate a plurality of slides in at least one configuration in corresponding sample carrier retention devices. The sample carrier retainment assemblies, are utilized in the processing of samples as further described below. It should be further noted that the sample carrier retainment assembly can be removably configured with the drawers, and may be stackable or nested within other retainment assemblies.
 One or more drawers may be provided to accommodate processing materials such as reagent containers 3 for sample processing, also further described below. A processing material retainment assembly, such as a container rack may be utilized to accommodate reagent containers or other processing materials within each of drawers 6. Bottle inserts may be preferably configured with the retainment assembly to ensure proper processing material positioning within the processing material retainment assembly and the drawer.
 Multiple drawers allow for one or a plurality of sample processing protocols to be performed by the system 1. Past efforts at sample processing, as previously described, may have been limited to processing sequences for an entire batch of carriers within the system. The present invention, however, in part by providing a plurality of drawers and carrier retainment assemblies, may allow for multiple batch processing, including real-time or adaptive capabilities for multiple batch processing, as further described below.
 The system may access, use and wash multiple probes or syringes for pipetting or otherwise aspirating fluids required for the staining of samples mounted or otherwise presented on slides. To eliminate cross contamination a system with a single reusable probe may wash the probe between each fluid applied. The task of washing the probe can have a large impact on the throughput of the overall system. The present invention may allow for multiple probes to be available to the system for use. The system may continuously have a clean, uncontaminated, sterilized, or an unused probe available to use and sample processing is not impacted by the required cleaning routine. The cleaning routine may be necessary to eliminate the possible cross contamination of fluids and, in some embodiments, may take up to about 1 minute to accomplish. The cumulative impact of the cleaning routine on a series of processing steps can add time to the throughput capabilities of the system. The addition of multiple probes or syringes may eliminate this impact and significantly decreases the time required to process the samples.
 Embodiments of the present invention comprise a mixing station or reagent mixer 9 (best shown in FIGS. 4 and 5). The system may mix component fluids, such as dyes, buffers, or other processing materials, preferably on demand and as the processing steps and protocols dictate. Fluids required during the processing steps may sometimes need to be mixed with other fluids to create a final activated fluid. However, the activity levels of these mixtures can be time sensitive and may therefore only be effective for a short period of time. The on demand mixing of fluids is advantageous in that it allows the fluids to be mixed immediately before being used. The syringe or probe 10, in preferred embodiments, will aspirate fluids into and from the mixing station 9 to mix component fluids. A rinse may further be dispensed into the mixing station to sterilize the station.
 As an example a presently preferred embodiment of a sample processing apparatus, also called a staining apparatus 1, according to the invention is shown in FIGS. 1 and 2. The sample processing apparatus 1 comprises a rectangular frame 4 surrounding a first station 2 comprising an array of compartments wherein each compartment a reagent vial 3 is placed, and a second station 5 wherein a number of separate racks 6 (which may be a drawer) is placed, and where each rack comprises a number of microscope slides 7 mounted side by side in the rack 6. In the embodiment shown, each rack may hold up to 8 slides, but the rack may be designed to hold any suitable number of slides. With eight racks arranged side by side, the shown embodiments may hold up to 64 slides 7 each having a sample, e.g. a tissue mounted on the upper side of the slide, so that reagent may be applied from above to the sample on each slide.
 A robot arm 20 in FIG. 1 for moving a probe 10 in X and Y (as well as Z) direction as indicated by the arrows X and Y is arranged above the frame 4 of the sample processing apparatus. The robot arm may is therefore position the probe 10 above all reagent vials 3 as well as above all the microscope slides 7, and may further operate the probe 10 to aspirate portions of reagent contained in any of the vials 3, to transfer the portion of reagent and apply it to any of the slides 7 in order to provide a selected staining or treatment of the sample on each slide 7. By use of suitable control means e.g. a computer (not shown) having the appropriate software and input data for the purpose, this staining apparatus I is able to automatically staining or treating samples requiring different staining or treatment reagents and processes.
 The same staining apparatus viewed from below the robot arm is shown in FIG. 2, disclosing the probe 10 being manipulated by the robot arm. The probe 10 is raised to an upper position (in a Z direction where it is clear of the vials 3 underneath the probe 10, but the robot comprises means (not shown) for lowering the probe 10 in order to dip the probe tip 211 into the content of a selected reagent vial 3 and to aspirate a selected amount of reagent for the selected staining or treatment process.
 The staining apparatus 1 of the present embodiment further comprises at least one probe washing station 8 and a reagent mixer 9, and the robot arm is furthermore arranged to transfer the probe to the washing station 8 as well as to the reagent mixer 9. The reagent mixer 9 will be described in detail below with reference to FIGS. 4 and 5.
 The apparatus comprises a reagent mixer 9 having a mixing cup 213 wherein two or more selected reagents may be placed by means of the robot arm and the probe 10. The reagent mixer 9 thereby provides on-board mixing of any reagents contained in the reagent vials 3, and thereby more staining processes, e.g. staining requiring the use of mixing of insoluble reagents, or reagents which may only be effective a short time after mixing, are facilitated to be performed automatically within the staining apparatus without the requirement of human interaction.
 The mixer 9 comprises a mixing cup 213 for receiving reagents released from the probe 10 or 110. The mixing cup 213 is placed into a holder 215 by means of a complementary snap fitting means 216 and 217 arranged on the inside of the holder 215 and the outside of the mixing cup 213, respectively. A motor 218 is arranged for rotating the holder 215 and thereby the mixing cup 213, either intermittently clockwise and anticlockwise in order to provide a mixing of reagents contained in the mixing cup, or by spinning the holder 215 and thereby the mixing cup 213 in order to fling out waste reagents or cleansing liquid from the mixing cup 213.
 For the latter purpose, the mixing cup 213 is preferable provide with sidewalls 220 extending upwardly and outwardly from the bottom 219, e.g. forming a frusto-conical cavity, and the mixing cup 213 has an upper rim 214 allowing the reagents to escape from the mixing cup 213 during the spinning process.
 The reagent mixer 9 furthermore comprises a housing 221 having sidewalls 222 surrounding at least the rim 214 of the mixing cup 213 and thereby forming splash faces for collecting any liquid flung out from the mixing cup 213. The housing also comprises a lid 223 for enclosing a space 224 surrounding the mixing cup 213 in order to avoid reagent spills outside the space 224. The lid 223 has a central opening allowing reagents from the probe 10 to be dispensed into the mixing cup 213 from above the reagent mixer 9 as well as allowing the probe 10 to enter the mixing cup 213 for collecting the mixed reagents.
 According to a preferred embodiment the housing also comprises a hose connection 227 for draining waste reagent or cleansing liquid from the space 224, and a tap 226 is arranged for dispensing cleansing liquid into the mixing cup 213 when required.
 In an alternative embodiment a releasable connection 212 is provided between the probe 10 and the robot arm, enabling the replacement of the probe 10 held by the robot arm by placing the probe 10 in one of a number of free washing stations 8, where it is released by the releasable connection 212, and where a new probe 10′ is connected to the robot arm by means of the releasable connection 212.
 Having the appropriate input data, the control means of the apparatus operates the robot arm to commence a staining or treatment run by firstly moving the probe to a first reagent vial 3, into which the probe tip 211 is inserted into the liquid and is aspirated into the probe 10 in an amount corresponding to the number of samples to be stained or treated, in accordance with the input data provided to the control means.
 The probe 10 is subsequently, in a first operating mode moved by the robot arm towards the slide rack system 5 in which the slides 7 are mounted. The slides 7 are situated with the surface horizontally oriented and the probe 10 releases the required amount of reagent on the appropriate slides in accordance with the input data. Alternatively, the probe 10 is in a second operating mode moved by the robot arm towards the reagent mixer 9 where it releases the reagent into the cup 213 of the reagent mixer 9, and is subsequently moved to the probe washing station 8, where the probe 10 is either washed or—in the alternative embodiment—released into a free washing station 8, and another probe situated in another washing station is connected to the robot arm. The robot arm moves the new clean probe to a second selected reagent vial 3 for collecting a selected amount of reagent from the second vial 3, and the probe is thereafter by means of the robot arm moved to the reagent mixer 9, where the reagent in the probe is dispensed into the cup 13 of the mixer containing the first selected reagent. The second operating mode can according to the invention be commenced several times if more than two reagents are to be mixed for a specific staining or treatment process.
 The reagent mixer 9 mixes the reagents in the cup 213 thereof, and a clean probe 10 picked up from the washing station 8 by the robot arm is lowered into the cup 213 of the reagent mixer 9 to collect the mixed reagents, where after the robot arm moves the probe 10 towards the second station 5 containing the slides 7, at which the probe 10 releases the required amount of mixed reagent on selected slides 7 in accordance with the input data.
 The robot arm with probe 10 is subsequently directed to a free washing station 8, and the probe 10 is either washed or alternatively replaced by a clean probe, where after the process in accordance with the first or the second operating mode may be repeated or continued with a new reagent or reagent mixture.
 The present invention is highly suitable for on-board mixing in an automated cytological/IHC/ISH instrument.
 It should be understood that by having an inner cup with smooth surface and no sharp edged, cleaning and washing is made easy. Other mixing devices using propellers or baffles or similar, all have large surface areas, edges and concavities, whereto reagents may adhere, whereby thorough washing becomes difficult, possibly resulting in unwanted carry-over.
 By design, the shape of the cup allows debris, fines, precipitates or other solids of both high and low density to be centrifuged up and out of the cup at high rotation speeds. Advantageously the speed may be controlled by control means operating according to the processing protocol carried out for the samples present in the apparatus, i.e. if the reagents present in the mixer cup have high viscosity it may be advantageous applying a very high speed of rotation to ensure that all reagents are removed from the cup.
 Also, the shape of the cup allow for the specific separation of immiscible liquid phases, by first removing the liquid with the highest density during centrifugation. It should be understood that the shape of the cup makes the mixing almost independent of the volume. The mixing action is the same for a wide range of volumes in the same cup. In contrast, the mixing action of e.g. a propeller mixer is depending on e.g. the volume of reagents, propeller size and container size.
 The rotating action of the cup allows air to escape from the mixture and prevent foaming. The rotating action can suppress the formation and build-up of foam by forcing the air/liquid foam down to the liquid surface.
 Preferably the rotation pattern (speed and direction) is controlled by controlling means, such as a computer, according to the sample processing protocol, thereby optimising the quality the mixing in the mixer cup in respect to the reagents present in the mixer cup, e.g. in such manner that the formation and build up of foam is suppressed.
 The rotating action of the cup does not allow much air from the atmosphere to be sucked down in the reagent mixture. This will limit the pollution and e.g. oxidation of air sensitive reagents. Other methods of mixing, like the action of propellers, can draw air down into the liquid during mixture.
 It should be understood that by changing the direction of the rotation, the mixing action could be changed from being very gentle to being very vigorous. Both changing the speed and direction of the rotation and a combination of rotations with variable speed, various speeds, stops and change of direction can control the flow pattern in the cup.
 Also, the cup can be covered with a neutral gas like the noble gasses, nitrogen, and carbon dioxide or similar to further protect the reagents during mixing. Preferable, the protective gas is heavier than atmospheric gas. The layer of protective gas can easily be added and removed, and can cover any of the volumes the cup can hold.
 By using an on board mixing device, the reagents mixing may be done in a batch-mode to make mixtures for treating multiple samples.
 Also, the on board mixing allow for large dilution ratios and the possibility to dilute or mix reagents, using only a small portion of the mixture for treatment of samples, and discarding the rest of the mixture. This is advantageous, as some dilutions ratios are very large, and too small volumes of the concentrated reagent cannot easily be accurately measured and added. Often a minimum volume of reagent to be measured is defined. The on board cup mixing design allow for a very high degree of flexibility in the staining protocol.
 As can be easily understood from the foregoing, the basic concepts of the present invention may be embodied in a variety of ways. It involves both mixing techniques as well as devices to accomplish the appropriate mixer element. In this application, the mixing techniques are disclosed as part of the results shown to be achieved by the various devices described and as steps which are inherent to utilization. They are simply the natural result of utilizing the devices as intended and described. In addition, while some devices are disclosed, it should be understood that these not only accomplish certain methods but also can be varied in a number of ways. Importantly, as to all of the foregoing, all of these facets should be understood to be encompassed by this disclosure.
 The discussion included in this application is intended to serve as a basic description.
 The reader should be aware that the specific discussion may not explicitly describe all embodiments possible; many alternatives are implicit. It also may not fully explain the generic nature of the invention and may not explicitly show how each feature or element can actually be representative of a broader function or of a great variety of alternative or equivalent elements. Again, these are implicitly included in this disclosure. Where the invention is described in device-oriented terminology, each element of the device implicitly performs a function. Apparatus claims may not only be included for the device described, but also method or process claims may be included to address the functions the invention and each element performs. Neither the description nor the terminology is intended to limit the scope of the claims that will be included in any subsequent patent application.
 It should also be understood that a variety of changes may be made without departing from the essence of the invention. Such changes are also implicitly included in the description. They still fall within the scope of this invention. A broad disclosure encompassing both the explicit embodiment(s) shown, the great variety of implicit alternative embodiments, and the broad methods or processes and the like are encompassed by this disclosure and may be relied upon when drafting the claims for any subsequent patent application. It should be understood that such language changes and broader or more detailed claiming may be accomplished at a later date or in the event the applicant subsequently seeks a patent filing based on this filing. With this understanding, the reader should be aware that this disclosure is to be understood to support any subsequently filed patent application that may seek examination of as broad a base of claims as deemed within the applicant's right and may be designed to yield a patent covering numerous aspects of the invention both independently and as an overall system.
 Further, each of the various elements of the invention and claims may also be achieved in a variety of manners. Additionally, when used, the term “element” is to be understood as encompassing individual as well as plural structures that may or may not be physically connected. This disclosure should be understood to encompass each such variation, be it a variation of an embodiment of any apparatus embodiment, a method or process embodiment, or even merely a variation of any element of these. Particularly, it should be understood that as the disclosure relates to elements of the invention, the words for each element may be expressed by equivalent apparatus terms or method terms—even if only the function or result is the same. Such equivalent, broader, or even more generic terms should be considered to be encompassed in the description of each element or action. Such terms can be substituted where desired to make explicit the implicitly broad coverage to which this invention is entitled. As but one example, it should be understood that all actions may be expressed as a means for taking that action or as an element which causes that action. Similarly, each physical element disclosed should be understood to encompass a disclosure of the action which that physical element facilitates. Regarding this last aspect, as but one example, the disclosure of a “mix element” should be understood to encompass disclosure of the act of “mixing”—whether explicitly discussed or not—and, conversely, were there effectively disclosure of the act of “mixing”, such a disclosure should be understood to encompass disclosure of a “mix element” and even a “means for mixing” Such changes and alternative terms are to be understood to be explicitly included in the description.
 Any patents, publications, or other references mentioned in this application for patent are hereby incorporated by reference. In addition, as to each term used it should be understood that unless its utilization in this application is inconsistent with such interpretation, common dictionary definitions should be understood as incorporated for each term and all definitions, alternative terms, and synonyms such as contained in the Random House Webster's Unabridged Dictionary, second edition are hereby incorporated by reference. Finally, all references listed in the list of References To Be Incorporated By Reference or other information statement filed with the application are hereby appended and hereby incorporated by reference, however, as to each of the above, to the extent that such information or statements incorporated by reference might be considered inconsistent with the patenting of this/these invention(s) such statements are expressly not to be considered as made by the applicant(s).
 Thus, the applicant(s) should be understood to have support to claim and make a statement of invention: i) each of the mixing devices as herein disclosed and described, ii) the related methods disclosed and described, iii) similar, equivalent, and even implicit variations of each of these devices and methods, iv) those alternative designs which accomplish each of the functions shown as are disclosed and described, v) those alternative designs and methods which accomplish each of the functions shown as are implicit to accomplish that which is disclosed and described, vi) each feature, component, and step shown as separate and independent inventions, vii) the applications enhanced by the various systems or components disclosed, viii) the resulting products produced by such systems or components, ix) each system, method, and element shown or described as now applied to any specific field or devices mentioned, x) methods and apparatuses substantially as described hereinbefore and with reference to any of the accompanying examples, xi) the various combinations and permutations of each of the elements disclosed, and xii) each potentially dependent claim or concept as a dependency on each and every one of the independent claims or concepts presented.
 With regard to claims whether now or later presented for examination, it should be understood that for practical reasons and so as to avoid great expansion of the examination burden, the applicant may at any time present only initial claims or perhaps only initial claims with only initial dependencies. Support should be understood to exist to the degree required under new matter laws—including but not limited to European Patent Convention Article 123(2) and United States Patent Law 35 USC 132 or other such laws—to permit the addition of any of the various dependencies or other elements presented under one independent claim or concept as dependencies or elements under any other independent claim or concept. In drafting any claims at any time whether in this application or in any subsequent application, it should also be understood that the applicant has intended to capture as full and broad a scope of coverage as legally available. To the extent that insubstantial substitutes are made, to the extent that the applicant did not in fact draft any claim so as to literally encompass any particular embodiment, and to the extent otherwise applicable, the applicant should not be understood to have in any way intended to or actually relinquished such coverage as the applicant simply may not have been able to anticipate all eventualities; one skilled in the art, should not be reasonably expected to have drafted a claim that would have literally encompassed such alternative embodiments.
 Further, if or when used, the use of the transitional phrase “comprising” is used to maintain the “open-end” claims herein, according to traditional claim interpretation. Thus, unless the context requires otherwise, it should be understood that the term “comprise” or variations such as “comprises” or “comprising”, are intended to imply the inclusion of a stated element or step or group of elements or steps but not the exclusion of any other element or step or group of elements or steps. Such terms should be interpreted in their most expansive form so as to afford the applicant the broadest coverage legally permissible.
 Finally, any claims set forth at any time are hereby incorporated by reference as part of this description of the invention, and the applicant expressly reserves the right to use all of or a portion of such incorporated content of such claims as additional description to support any of or all of the claims or any element or component thereof, and the applicant further expressly reserves the right to move any portion of or all of the incorporated content of such claims or any element or component thereof from the description into the claims or vice-versa as necessary to define the matter for which protection is sought by this application or by any subsequent continuation, division, or continuation-in-part application thereof, or to obtain any benefit of, reduction in fees pursuant to, or to comply with the patent laws, rules, or regulations of any country or treaty, and such content incorporated by reference shall survive during the entire pendency of this application including any subsequent continuation, division, or continuation-in-part application thereof or any reissue or extension thereon.
1. A sample processing apparatus for treating samples arranged on a carrier comprising:
- a vial station for containing at least two reagent vials,
- a carrier station arranged for intermediate storage of a plurality of carriers,
- a probe drive adapted to move a probe,
- wherein the probe drive is arranged to aspirate a portion of reagent from a selected reagent vial of the vial station with a probe and to apply reagent to a selected carrier of the carrier station,
- a reagent mixer having a mixing cup adapted to receive two or more reagents and mix element adapted to mix the reagents in the mixing cup, wherein said reagent mixer is adapted to dispense the reagent mixture from the mixing cup to a selected carrier of the carrier station.
2. A sample processing apparatus according to claim 1, wherein the probe drive is arranged to apply the reagent mixture from the mixing cup to selected carrier of the carrier station.
3. A sample processing apparatus according to claim 1 or 2, wherein the probe drive is arranged to aspirate portions of reagents from at least two selected reagent vials of the vial station and dispense said portions of reagents into the mixing cup.
4. A sample processing apparatus according to any of claims 1 to 3, wherein the reagent mixer further comprises cup drive arranged for cyclic movement of the mixing cup so as to mix reagents contained in the mixing cup.
5. A sample processing apparatus according to claim 4, wherein the cyclic movement is a rotation of the mixing cup and wherein the rotation is an intermittent rotation in a clockwise and in an anticlockwise direction.
6. A sample processing apparatus according to claim 5, wherein the rotation takes place about a substantially vertical axis.
7. A sample processing apparatus according to claim 4, wherein the movement is a combination of rotations with variable speed, various speeds, stops and change of direction, wherein the rotations is controlled by control element according to the sample processing protocol for the sample(s) processed in the apparatus.
8. A sample processing apparatus according to claim 3, wherein the mixing cup has inner walls extending upwardly and outwardly from a bottom part of the mixing cup, and the cup drive is capable of rotating the mixing cup at an angular speed sufficient to fling reagents contained therein out of the mixing cup.
9. A sample processing apparatus according to claim 8, wherein the reagent mixer comprises a waste reagent collecting chamber having a sidewall part laterally surrounding the mixing cup, and wherein waste reagent collecting chamber is arranged to collect reagents flung out of the mixing cup by rotation of the cup.
10. A sample processing apparatus according to claim 3, wherein the reagent mixer further comprises a mixing cup holder adapted to receive and support the mixing cup in a releasable manner.
11. A method of fully automated treating of samples arranged on a carrier of a sample processing apparatus controlled by control element, wherein the method comprises the steps of:
- arranging a plurality of carriers intermediately in a carrier station, each carrier having a sample arranged thereon,
- dispensing a portion of a first reagent selected from a plurality of reagents to a mixing cup,
- dispensing a portion of a second reagent selected from a plurality of reagents to the mixing cup,
- mixing the reagents in the mixing cup,
- moving the probe to the mixing cup with a probe drive,
- aspirating a portion of the mixed reagents from the mixing cup with the probe,
- moving the probe to a selected one of said carriers, and
- dispensing the mixed reagents to the selected carrier,
- so as to perform a treatment of the sample arranged on the selected carrier.
12. A method according to claim 1 1, wherein the steps of dispense portions of the first and the second reagents comprises the steps of:
- moving a probe to a first, selected reagent vial with the probe drive,
- aspirating a portion of the first reagent from the first reagent vial with the probe,
- moving the probe to the mixing cup with the probe drive,
- dispensing the portion of the first reagent to the mixing cup,
- moving a probe to a second, selected reagent vial with the probe drive,
- aspirating a portion of the second reagent from the second reagent vial with the probe,
- moving the probe to the mixing cup with the probe drive, and
- dispensing the portion of the second reagent to the mixing cup.
13. A method according to claim 11 or 12, further comprising the step of controlling the rotation pattern according to the sample processing protocol thereby optimising the quality the mixing in the mixer cup in respect to the reagents present in the mixer cup.
14. A method according to claim 11 or 12, further comprising the step of adding a protective gas covering the reagent mixture in the mixer cup.
15. A method according to claim 14, wherein the protective gas is selected from the the group consisting of noble gasses, nitrogen, and carbon dioxide.
Filed: Dec 19, 2003
Publication Date: Dec 30, 2004
Applicant: DakoCytomation Denmark A/S (Glostrup)
Inventors: John Favuzzi (Santa Barbara, CA), Marc Key (Ojai, CA), Lars Winther (Smoerum), Ole F. Rasmussen (Malov), Bob Lathrop (San Jose, CA)
Application Number: 10741628
International Classification: G01N035/02;