# Patent

## Title
Isolated communication sample processing system and methods of biological slide processing

## Abstract

A sample processing system 101 that may be automated and methods are disclosed where a number of sample processing systems 101, such as stainer, may be connected to a number of separate full function computers 181 through a stainer network 183 that may be isolated from other communication traffic. A network configuration may permit scalability and addressability so that additional sample processing systems 101, additional separate full function computers 181, and additional other devices such as label printers 200 may be easily added to the system. One or more remote information links 171 may be provided so that information transfer on a continuous or perhaps constant basis can be accommodated.

## Background
This application is the United States National Stage of International Application No. PCT/US2003/041022, filed Dec. 22, 2003, which claims the benefit under 35 U.S.C. 119(e) of U.S. Provisional Application No. 60/435,601, filed Dec. 20, 2002; and priority from International Application No. PCT/US2003/040974, filed Dec. 19, 2003, International Application No. PCT/US2003/040591, filed Dec. 19, 2003, International Application No. PCT/US2003/040519, filed Dec. 19, 2003, International Application No. PCT/US2003/040518, filed Dec. 19, 2003, and International Application No. PCT/US2003/040880, filed Dec. 22, 2003; each hereby incorporated by reference.


TECHNICAL FIELD
This application relates to the field of sample processing systems and methods of transferring information relative to processing of samples or the process system. 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 interruptible processing of samples and carriers. Embodiments may further relate to control systems for sample processing and data input, acquisition, maintenance, and 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.
BACKGROUND
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 including but not limited to microscope slides. 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.
Immunohistochemistry, histological, or histopathology applications, for example, may require processing sequences or protocols that comprise steps such as deparaffinization, target retrieval, reagent application, and staining, especially for in-situ hybridization (ISH) techniques. 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. Even when performed automatically, there have been inefficiencies in such systems. Attempts have been made to automate sample processing to address the need for expedited sample processing and a less manually burdensome operation. However, such previous efforts may have not fully addressed certain specific 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 practical information input and process definition entry capabilities; 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 and U.S. Pat. No. 5,839,091, have not afforded the various advantages and other combinations of features as presented herein.
One of the various aspects that may be significant to users of automated process systems is that of permitting a variety of communication transfers to, from, and within a system that can be easily expanded while assuring the integrity of the process and process information. These aspects can also be important when allowing changes to the processing while it is ongoing. In addition, operators often have needed to be physically present in order to act upon or simply monitor operations of a system. The present invention seeks to reduce such effects to some degree and seeks to provide a system that may be considered more user, operator, supplier, or manufacturer friendly and may be adaptable to real-world conditions and events.
DISCLOSURE OF INVENTION
The present invention presents an automated sample processing system that may greatly improve operation of automated sample processing from several perspectives. It can provide for a variety of communications interactions and modes. Scalability can be included so that additional resources, such as additional processing systems, additional terminals, and even additional communication access can be easily added to the system. To achieve the goal of assuring a good processing result stand alone capability with fault tolerance in the event of an unavailability or even a breakdown in communications can be included. In providing this disclosure, it should be understood that the various examples and designs disclosed for sample processing and other disclosed techniques, are not meant to limit the present invention to any particular embodiment, whether apparatus, method, or otherwise. These descriptions are provided rather to describe various sample processing techniques in a manner in which the present invention can be understood. The descriptions incorporated by reference and the various examples should not be construed to limit the present invention to only such techniques. This disclosure, however, may be understood to incorporate the various techniques in the context of the various embodiments of the present invention.
The techniques and systems of sample processing are addressed in a fashion that may provide the processing of one or more samples or of a plurality of groups of one or more samples in sequential or non-sequential fashion. Processing of samples may be determined by the protocol to be followed for each sample or a protocol for multiple samples. Aspects of the present invention may be especially applicable to sample processing having one or a plurality of processing steps to be performed on one, a portion, or an entirety of samples, such protocols identified in some instances by individual carriers presenting the samples or by the individual samples themselves. As mentioned, the present invention may be especially applicable to immunohistochemistry (IHC) techniques, as well as in-situ hybridization (ISH) and fluorescent in-situ hybridization (FISH), special staining of samples, and microarrays; especially techniques incorporating target retrieval, deparaffinization, pretreatment, or the staining of samples. Furthermore, embodiments may be directed to processing sequences addressing issues of processing control.
Embodiments of the invention may further relate to automated control and communication systems for sample processing. Embodiments may be directed to remote, isolated, and/or continuous data transfer, acquisition, input, maintenance, and retrieval for sample processing, as well as information sharing of processing protocol and processing information, and scalable designs to permit users to easily configure a system as desired.
To disclose the foregoing and other objects and in accordance with the purposes of the present invention, as broadly embodied and described herein, the present invention is characterized in various claims and in explanatory disclosure. None of these should be understood as limiting. Further, all claims presented at any time are incorporated in the specification to afford all opportunities of presentation. Claims potentially to be pursued for some of the initially presented aspects of the invention may include any aspects described.
To achieve the foregoing and other objects of invention, and as may be further disclosed and claimed throughout this description, the invention may comprise an automated sample processing system comprising a plurality of drawers, a plurality of sample carrier elements that may even be each removably configured with one of the drawers, and an adaptive or other sample processing control system. The sample carriers may be both movable and removable. The sample processing control system may automate the sample processing system and may provide for a variety of communication transfers to/from/and within an overall system so that one or more samples may be processed according to one or more protocols, potentially indicated by information on slides or otherwise input to the system. This sample processing may comprise one or more sampling protocols and steps, such as deparaffinization, target retrieval, and staining.
A sensor may be provided in some embodiments that may automatically identify information from one or more samples, sample carriers, or slides. In embodiments, protocol information may be provided or made available by the sample processing control system. The sample processing system may then process one or more samples or perhaps slides, or one or more batches of slides, concurrently, sequentially, or in any other temporal fashion, potentially in accordance with protocol information previously provided for a sample by a user or other decision maker. This information can then be made available for use by the sample processing control system. Sample batches or individual slides may even be inserted or removed during processing protocol steps by the control and monitoring accomplished by the adaptive sample processing control system.
Another embodiment of the present invention that may achieve the foregoing and other objects of invention may comprise a method of sample processing, comprising the steps of: accessing at least one of a plurality of samples or sample drawers, providing at least one sample carrier or perhaps a sample carrier retainment assembly configured with at least one sample, configuring at least one of the drawers with the at least one sample carrier, and adaptively processing the sample. The step of processing or perhaps even adaptive processing may be applied to automate the processing of samples and may allow for either or both continuous or batch processing of samples or slides. It may also afford multiple independent sample or slide processing and in some embodiments slide processing to process each slide independently.
Embodiments of the invention may further comprise a method of automated sample processing, comprising the steps of: acquiring or accepting or accessing information such as protocol or reagent information, transmitting such information to at least one sample processing system or even a stand alone processing system over an isolated communication functionality, and processing samples. Furthermore, embodiments may provide for handling, maintaining, sharing, and using the sample processing information. These and other aspects may be provided for individual samples or multiple batch processing, and in a real-time manner. It may also be accomplished in and adaptive manner, perhaps for multiple batch processing or the like.
Again, as mentioned, many of the various aspects of the present invention are applicable to immunohistochemistry (IHC), as well as in-situ hybridization (ISH) and fluorescent in-situ hybridization (FISH), special staining of samples, microarray processes, and techniques incorporating target retrieval or the staining of samples. Furthermore, embodiments are directed to processing sequences addressing issues of processing control, and may be particularly applied to slide processing systems.



BRIEF DESCRIPTION OF THE DRAWINGS
The accompanying figures, are incorporated in and form a part of the description, illustrate some of the preferred embodiments of the present invention. Together with the written description and disclosures of the specification, they serve to explain principles of the invention and to enable each of the disclosed embodiments.
FIG. 1 is a depiction of an embodiment of an overall system incorporating some of the features of the invention.
FIG. 2 is a depiction of an embodiment of a portion of a sample carrier assembly of one embodiment of the invention.
FIG. 3 is a depiction of an embodiment of a robotic movement aspect of one embodiment of the invention.
FIG. 4 is a flow chart of some representative process steps of an embodiment of the invention.
FIG. 5 is a block diagram of an embodiment of the invention.
FIG. 6 is a depiction of an embodiment of a device incorporating some of the features of the invention.
FIG. 7 is a depiction of an embodiment connecting one stainer with one manager & server and one label printer.
FIG. 8 is a depiction of an embodiment connecting multiple stainers with multiple managers and multiple label printers.
FIG. 9 is a depiction of an embodiment connecting a system to a lab network and lab information system.
FIG. 10 is a block diagram showing some of the internal software features.
FIG. 11 is a description of representative deparaffinization steps of an embodiment of the invention.



BEST MODES FOR CARRYING OUT THE INVENTION
The following descriptions are provided to describe various embodiments of the present invention in a manner to facilitate a more detailed understanding some of the inventive features. 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. This description may further be understood to incorporate the various systems, techniques, and applications, both singularly and in various combinations consistent with the various inventive features and embodiments of the present invention. Accordingly, the following is a detailed description of a number of specific embodiments of the invention.
FIG. 1 shows one embodiment of a sample processing system 101 in accordance with the present invention. The sample processing system 101 is configured to achieve an appropriate sequence of events that achieves a desired result to some degree. In achieving this sequence in an automated fashion to some degree the sample processing system is deemed an automated sample processing system and achieves automatic processing of at least one sample. This automated sequence as well as other aspects of the invention may be controlled by hardware, software, or some combination of them to accomplish a desired sequence with limited human intervention. Regardless how achieved, the automated control may be provided by a process operation control system 171 (shown conceptually in FIG. 10) to direct the various activities. As shown in FIG. 10, this (as well as other functionalities discussed) may be software programming or subroutines; again, it may also include hardware or the like. Referring to FIG. 2, the sample 198 processed may be any material, but is most likely a biologic material such as a biological sample or a biological specimen, perhaps such as a histological sample, e.g. tissue and cell specimens, cells, collections of cells, or tissue samples, the definition to include cell lines, proteins and synthetic peptides, tissues, cell preps, cell preparations, blood, bodily fluids, bone marrow, cytology specimens, blood smears, thin-layer preparations, and micro arrays. It should also be understood to include slide-based biological samples. As used, a sample may be arranged on a carrier element 197 such as a slide, or microscope slide, or the like that may maintain the sample's position or integrity. The carrier element 197 may be configured to move and thus reposition the sample 198. As such, it may be considered a movable carrier element. In processing a slide, the automated sample processing system may serve as an automated slide processing system.
The automated sequence may involve a significant number of steps. In fact each process can itself require many automated movements to achieve its goal. Each of these types of operations or actions may be relevant to understanding an instrument's operation. Further, each of these types of operations or even a lesser set of significant events may be considered important details of the sample process operation. As explained later, it may be valuable to capture and make available historical or other information relative to a significant number of these actions such as all of these operations, some subset of these operations, one-half of these operations, one-third of these operations, or the like. Further, even the nature or type of the events that may be of interest may be varied. In general, any event that may indicate the propriety of operation or processing may be a subject. Naturally in order to achieve automated processing it will be necessary to schedule the various sample process or process operations desired. This can be achieved by an item of software or the like that acts as a multiple event scheduler 401 as shown in FIG. 10.
Referring to FIG. 1, a particular design of a system may include cabinet sections 102 that may 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 also comprise a plurality of drawers 104 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 carrier retainment assemblies that hold one or, most likely, a number of the particular carriers, slides, or samples involved.
As shown in FIG. 2, in holding slides the carrier retainment assembly serves as a slide retainment assembly 106. There may also be carrier racks, modules, or magazines encompassed within each of the two broad terms. This is merely one embodiment of a sample carrier retainment assembly. The slide retainment assembly, and indeed the generic carrier retainment assembly may comprise a slide rack, module, or a number of magazines. The slide retainment assembly 106 may be configured to accommodate a plurality of slides in at least one configuration in corresponding sample carrier retention devices 108. 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 104, and may be stackable or nested within other retainment assemblies. One embodiment of such a system is shown in FIG. 6.
The general sample processing system, and even one or more drawers 110 in the sample processing system may accommodate processing materials such as reagent containers 199 for sample processing, also further described below. A processing material retainment assembly, such as a container rack 111, shown in FIG. 6, may be utilized to accommodate reagent containers 199 or other processing materials within each of drawers 110. These drawers may be lockable through programming to prevent access during certain stages of automatic operation. 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 110 may be included to allow for one or a plurality of sample processing protocols to be performed by the system 201. 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 interruptible individual, batch, or multiple batch processing, including real-time or adaptive capabilities, as further described below.
Indicator elements 112 as shown in FIG. 1 may be provided to indicate a status and accessibility of the drawers and the carriers or materials within each drawer for an operator of the system. In one embodiment, visual indicators, such as light emitting diodes in preferred embodiments, may be used to indicate if a drawer is available, and perhaps unlocked, during operation of the sample processing system, and may indicate conditions such as a locked or open condition of a corresponding drawer, carrier capacity status of the drawer or of a carrier retainment assembly within the drawer, and chemical inventory status of the sample processing system, such as reagent loading status or capacity. A warning indication may be given by these or other indicator elements, as well as other indicative signals. One or a plurality of sensors may be utilized to determine the status of the drawer as indicated by the indicator elements 112 and to further provide processing status as further described below.
In accordance with the desire for an automated processing system, embodiments of the present invention may include robotic sample process functions or a robotic motion system 172 as shown in FIG. 6. This may be responsive to the process operation control system 171 and may involve a continuous, and perhaps even interactive, transfer of information to achieve the desired operation steps. The robotic motion system 172 may further comprise an arm 120 utilized in sample processing, potentially having robotic movement, and in some embodiments, Cartesian movement perhaps with orthogonal movement directions as shown in FIG. 1. Through the inclusion of a robotic motions system or the like, the system may provide an automated process operation capability that causes automated process operation events through robotic sample process functions. These may be responsive (a term intended to encompass any interaction, whether connected or not and whether directly or indirectly having an effect) to a number of perhaps stand alone devices such as stand alone stainers. As shown in FIG. 3, the arm 120 may comprise, in some preferred embodiments, one or more elements, such as an actuator probe 122, a syringe or probe 124, an optical sensor element 86 and a non-discrete or other volume fluid and/or air applicator. The actuator probe may be utilized in the configuration and manipulation of the carriers in sample processing, further described below. In some preferred embodiments, the actuator probe 122 configures and manipulates the configuration of slides in the sample carrier retention devices 108 by actuation of carrier adjustment element 130 (see for example FIG. 2), and in some embodiments, by contact with the slides. As mentioned, in some embodiments, manipulation or movement of the slides or the samples may be accommodated. This movement may result in a horizontal or vertical configuration of the slides to facilitate sample processing as described below.
As mentioned above, there may be a large number of process steps accomplished. As may also be appreciated from the nature of the processes envisioned, there may be uses of many different substances or the like. This conduct may generate or involve information that may be significant from an operational perspective. As such the present invention may provide the capability to accept, generate, provide, and transfer that information regardless of its nature. Aspects can broadly involve information to, from, or within the system. Regardless where the actual programming resides, the overall system can be designed to include an automatic sample process information transfer functionality configured to transfer information from a sample process system such as a stainer or conversely an automatic sample process system information transfer functionality configured to transfer information to a sample process system such as when information or changes are input to the system through a separate computer, such as a workstation or even a server. The information may be any type of information related to an aspect of sample processing, including but not limited to: refill information, inventory information, status information, backup information, off-site support information, sample input information, schedule input information, update information, real time status information, notice information (such as to an operator, administrator, supplier, or even manufacturer), and diagnostic information. Each of these may have a corresponding functionality, such as a subroutine or computer program that achieves the desired aspect. It may also involve the inclusion of an operationally-influential exteriorly-consequential information monitor 402 as shown generally in FIG. 10 to monitor and cause notification of a person of an aspect relative to the system. Thus the present invention may include an ability to transfer, generate, and even monitor information of a broad nature.
As previously mentioned, arm 120 may comprise syringe 124. The syringe 124 may be considered a probe in some embodiments, depending upon the requirements of protocols to be performed. Syringe 124 may be fluidically connected with and may interact with one or more of the following: rinse agents, such as water; potentially removable and fluidically connected containers for the aspiration of reagents, such as aspiration of reagents from containers and to the samples presented with the carriers; and blow off or other removal agents such as an air source. Syringe 124 may be utilized to pierce processing material containers such as reagent containers. In some embodiments, a reservoir may be provided with the arm 120 to allow for various volumes to be aspirated by syringe 124. The unique configuration of the reservoir allows for efficient cleaning and drying of the internal portions of the syringe while allowing for the accurate pipetting or otherwise aspiration of a wide range of volumes.
In preferred embodiments, the sample processing system 101 may include an automatic slide identification element. This may be controlled to achieve the act of automatically identifying a plurality of slides. This may also be more generic such as there may be some type of sensor element and it may even comprise an optical sensor 86, a reader or scanner, such as a CCD camera, utilized to determine status information of processing materials, such as reagents as well as to identify slides. The sensor element, for example, may read, detect, or otherwise determine information in the sample processing system 101, for example, from processing material containers, such as, for example, reading coded or perhaps encrypted information provided on the container to determine reagent type and reagent location within the system. The sensor element may also determine status information of sample carriers. For example, in some embodiments, slides configured with a slide retainment assembly may be provided with informational indicia, such as a code, that may indicate information about the sample presented on the slide or the processing protocol to be performed. The sensor element may read the code of the slide to determine the protocol to be performed for the particular slide and sample.
A cleaning station 140, shown in FIG. 1, may be included to clean elements of arm 120, and in preferred embodiments, may function to clean or otherwise remove completely the previously deposited reagent from the probe, or remove elements containing the internal and/or external surface of the probe and/or syringe 124. In one embodiment, the cleaning station may be configured to clean elements of arm 120, such as syringe 124, while such elements are configured with arm 120. The syringe may be cleaned, for example, with a water rinse through the syringe while the syringe is positioned at the cleaning station. In other embodiments of the present invention, the cleaning station 140 may be configured to allow a drop off and pick up of elements such as syringes for cleaning while allowing the processing throughput of the sample processing system to continue.
Embodiments of the present invention may comprise a mixing station 150, shown in FIG. 1. 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 mixture or cocktail. 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, or perhaps just-in-time mixing of fluids is advantageous in that it allows the fluids to be mixed immediately before being used. This may be coordinated with the scheduling functions discussed below to permit the simultaneous goals of on demand mixing with enhanced scheduling. The syringe or probe 124, in preferred embodiments, will aspirate fluids into and from the mixing station 150 to mix component fluids. A rinse may further be dispensed into the mixing station to sterilize the station.
In preferred embodiments, slides are movable and configurable in both vertical and horizontal positions as required for the pretreatment and staining process. This allows for the automation of the pretreatment and staining of slides in various manners, including pretreatment and staining as accepted in conventional manual laboratory methods. The slides are initially loaded into the carrier retention assemblies, such as slide racks, and drawers in the horizontal position. If pretreatment is required, such as deparaffinization, the system rotates the slide into the vertical position and lowers these samples into a processing tank, further described below, filled with the required fluids. In some embodiments, the slide rack is lowered to affect lowering of the slides (see FIG. 2). To perform the staining process on the slides, as described below, the system rotates or moves the slide to the horizontal position and a syringe or probe applies fluid to the sample, providing a horizontal staining of the sample. Each slide can be rotated independently allowing for the independent processing of different samples with different requirements.
In some embodiments, the individual fluids used for pretreatment may be contained in the system cabinet Deparaffinization fluids (except DI water) may be drawn into the processing tanks, then returned to their containers for reuse. On a periodic basis, the material in the “dirty” containers may be discarded. The “clean” containers may be moved up to the dirty position, and then fresh fluid added to clean position. DI water may be drawn from the large system DI water container, and discarded after each use. Target retrieval solution may be drawn from dedicated containers, and may be recycled or discarded after each use.
Returning to the aspect of monitoring or capturing information, an embodiment of the system may be designed to monitor replenishable supply information, such as the status of buffers, reagents, stains or the like. By monitoring for a potential need for replenishable supplies the system may remove at least one possibility for human error. Significantly, the system may also act to automatically notify any number of people relative to the information monitored. With respect to replenishable supply information, the system may notify a user, an operator, an administrator, or even a supplier of an actual, potential, or impending need to replenish supplies. As such the system may be considered as including an automatic notice element 404, or the like.
In a similar fashion, an embodiment of the system may monitor or capture information that is of interest to the continued or continuous operation of the device. By including a monitor of some sort, the system may facilitate not only enhanced reliability and continuous operation, but it may permit preventative activities. Naturally, it may use the automatic notice element 404 as a result of such activities to inform a wide range of persons of relevant issues, perhaps even providing advance notice to a person of upcoming predictable or estimated events. For items that may be very important there may even be multiple notices either concurrently or sequentially and as such the system may include a multiple advance expiration notice element. One type of information that may be monitored is historical information such as information of a statistical or past nature. This can be useful for operators who desire to know, prove, or have a record of what actions actually occurred in the system. The system can act to capture and store historical information. When multiple stand alone systems are included, such as in a networked configuration as discussed below, each stand alone system (meant to encompass any system that has the ability to perform all or perhaps some portion of its functions without any need for an outside element or interaction) may capture and store its own historical information, that is information about its own events or relative to it. This information, or at least part of it may then be transferred automatically to a server or other separate electronic location at convenient times or perhaps when there is a communication link available. To assure for the continued availability of such information, there may be included an array of multiple memory elements 701 which may actually be configured as a mirrored array. This may be responsive to the historical information generation element, such as data capture element 414 and may include a separate electronic location historical information transfer functionality 703 in response to an automatic separate location availability monitor 704. Cross data capabilities between separate stand alone systems may provide for a sharing of such resources and other information such as by the inclusion of a processing system interaction functionality 705. This may permit both interaction and communication of data between stainers or the like.
By having a data capture element 414, the system may generate data that may include or permit analysis or use of a variety of aspects, including but not limited to: number of occurrence data, part operation data, amount of usage data, and amount of material used data, statistical data or the like. Such data may, of course, have a like element, perhaps a subroutine, to do or generate the various function or data involved.
In some embodiments, an imaging device such as an optical sensor 86 or an image-capture 2-D optical sensor, perhaps a CCD camera, or the like, may be used to determine the position or identity of the sample on the slide, providing for greater accuracy during sample processing. The system may also generate or also monitor subject sample data. Relative to the imaging device, the system may monitor or perhaps capture image data, such a sample image data, substance image data, system image data, and even pre- and post-event image data. Each of these may be systematically stored, transferred or provided for some purpose.
The processing of samples may be accomplished according to some preferred embodiments as shown in FIG. 4 and FIG. 11 consistent with features of the present invention. Variants of these protocols and processing steps, or other processing steps, may be accomplished consistent with the present invention.
One processing sequence may broadly comprise the pre-processing of a sample, if needed, such as deparaffinization (as previously described), and further comprise target retrieval (as previously described), and sample staining.
In some embodiments, specifics of in-situ hybridization (ISH) may be addressed. Embodiments of ISH may require a small volume of reagent such as 15 microliters, to be placed on the sample. Heat control may be maintained between about 95-100 C and kept constant for a period of time. Temperature may then be lowered in a controlled manner.
Furthermore, fluorescent staining or tagging in IHC or ISH (FISH) may be performed consistent with the features of the present invention.
As mentioned, the sample processing system may automate the processing of samples mounted on carriers or slides. This configuration of the system allows for the flexibility for both continuous, interruptible, individual, and batch processing of slides with the design lending itself to meet established laboratory workflow demands. The multiple independent and redundant slide processing subsystems found within the system may also maintain its ability to process each slide independently.
The automatic processing may be achieved by designing a system with automated process operation capability or sequencing through at least some steps without human intervention. This may be controlled by or act in response to a process operation control system 171. This may be provided through hardware, software, or some combination of the two. One conceptual embodiment depicts some of the various capabilities in FIG. 10. Of course, the user needs the ability to specify the nature and sequence of the various steps or acts desired or even the appropriate priority or other scheduling parameters to be used. This can be accomplished by an input parameter capability 173 through the inclusion of even a sample process parameter input 173. Input can be provided on a separate computer or the like and can then be transferred through some electronic connection 176. Referring to FIGS. 7, 8, and 9, it can be understood that this connection may be with an element, such as a separate full function computer perhaps configured as a client or manager, or server, or otherwise programmed for operation with a sample process system and that is physically separate from the sample processing element such the stainer. By selecting an appropriate type of connection such as a scalable connection, it may be easy to establish a plurality of client, stainer, or other functionalities. This connection may be an address-based connection. Communication may involve the process of prompting address-based electronic communications programming to request specific activity, then transferring that request for specific activity to an appropriate element such as a stainer, conducting activity in accordance with that request, and transferring a response to the request. By using a networked communication design, all of this may involve an intermediate computer functionality or an intermediate computer response functionality (e.g., programming that acts to respond thereto), such as the manager and server functionality 500 shown in FIGS. 7 and 5. Appropriate programming to permit the stainer or other sample process system to respond to the intermediate computer functionality can be included. All such communication can occur repetitively and the system may use a continuous physically remote communication link such as by communicating to a separate computer or the like. Even if not always in use, information transfer capability may be constantly available, that is involving a open line that can accommodate information transfer at nearly any time (other than when sharing such resources). The communication link that may establish remote information transfer abilities may also be a transient link, such as a link activated through a dial-up phone line or the like. By permitting an embodiment to continuously transfer sample process information, that is, throughout various sequences of the overall processing events, both process integrity, processing data communication information functionality, and general processing information availability can be assured.
With respect to the input of information to the sample process system, input can be retained by the creation of stored parameter process data 174 so that the system can achieve the aggregate or perhaps plurality of process operations desired even if a connection were lost. In order to facilitate uninterrupted processing, the input parameter capability 173 may be configured as an independent process parameter input with respect to the process operation control system 171, such that acts caused by the process operation control system 171 are unaffected by any action with respect to the independent process parameter input. Further, the input parameter capability 173 may also be configured as an autonomous input functionality through the inclusion of an autonomous input element.
With the desired types of processing input, the system may act to automatically schedule the various events perhaps through a schedule element 605. These events may be considered as making up an aggregated event topology in that there is an aggregation of desired events and in that the events themselves present some topology or contour for a processing sequence. This topology may include only the events or it may include certain goals such as a particular prioritization or outcome desired. When using an initial input, the system may achieve scheduling of the events in the manner desired. Of practical importance may be the ability of an embodiment of the invention to permit and facilitate operator changes to the initial aggregated event topology. Significantly, these changes may be achieved dynamically, such as while other parts of the system are continuing processing. In facilitating changes while otherwise operating with little or no interruption, the system may act to achieve adaptive scheduling. This may begin as adaptive scheduling of an initial aggregated event topology and may evolve into adaptive scheduling of an altered aggregated event topology. This may occur on individual or perhaps stand alone devices, such as a stand alone stainer, or it may occur on an inter machine basis, such as by using an inter machine schedule indicium or an inter machine schedule element. Regardless, it should be understood that the scheduling of an altered topology may occur after commencing an initial automatic processing routine.
The alteration of the aggregated event topology may include any variety of actions that effectively alter an initial setup. These may include but are not limited to: altering the aggregate, such as perhaps adding a sample, deleting a sample, changing a sample, or altering the topology such as accepting a user change input such as merely a change in priority. They may also include accepting a temporary user change such a change that a user wants to see the effect of but may not wish to implement. Thus the system may include a sample addition element, a sample deletion element, more generally a sample change element 601, or a temporary user change element, each of which may be considered as creating some type of altered aggregated event topology. To permit a user decision embodiments may include functionality or subroutines for activating a user change or undoing a user change. These may be considered a user change activation element or a user change undo element. Such selection may be presented in conjunction with a results display element 602 of some sort such as an effect synopsis display element, a temporal impact display element (e.g., the time impact on one or more samples to be processed as a result of the alteration), and even an estimated temporal impact display element, whereby the time effect is only estimated.
As mentioned, the items to be processed or the sequence for processing may be altered. In embodiments, this may occur at any time and can result in the interrupting of processing to accept the change and then a resuming of the processing with the altered aggregate topology. This can involve changing at least one aspect of sample processing that can cause a rescheduling of the robotic sample process functions. In order to accomplish this, there may be included a sample process change functionality 708, a process interrupt functionality 603, a process resume functionality 707, and a robotic sample process reschedule functionality 709. To accommodate any schedule, the system may be able to provide a buffer or the like to permit time flexibility in the sequencing of actions. To apply additional buffer, the system may thus include an additional buffer functionality 710. Upon an alteration in the aggregated event topology, rescheduled sequence may be used to interrupt or may provide an interrupt 603 relative to the initial sequence and to thereafter continue revised automatic processing according to the altered aggregated event topology. As can be understood, this may be accomplished without completing the initial automatic processing. The rescheduling may be programmed to achieve a variety of results and then to compare and determine a “best” depending on how the operator or system defines that goal. Achieving a variety of results can be accomplished by simulating runs or perhaps a portion of a run and comparing the results of that simulation. The simulation may be of varied sequences set up according to certain parameters as explained below. By so doing, embodiments may include varied-parameter robotic control simulation functionalities, that is programming that simulates robotic operations based on differing parameters. These varied-parameter robotic control simulation functionalities may be responsive to the aggregated sample process input by acting on the data the input creates. Specifically, the system may run multiple simulations, perhaps at high speed, for the same aggregated event topology with each simulation using different criteria to determine the sequence of steps. The results of these simulations may be indicium that can be used and compared. Comparison may be achieved by an automated process simulator comparator which may look at any indicium resulting from the particular simulation being considered. From the indicium, a decision may be made and a particular set of parameters may be determined to cause an enhanced, if not optimium, sequence for a desired goal. These parameters may then be used in a preferred functionality robotic control generator which may then actually create the sequence that is used for the desired process operation. In this fashion, the system may have a process generator that is responsive to the automated process simulator comparator and from which an automated process functionality may be created.
As may be understood by the above, rescheduling due to an altered aggregate event topology may be impacted by a number of factors. As but one example it may be understood in shortening time for overall processing, the location of a particular substance or a particular sample may be important; the further between samples or substances, the slower the processing. Because of this type of factor, it is possible that the system may actually consider, simulate or otherwise assess factors and may suggest actions that may yield desired results. For example, the system may communicate, perhaps across a continuous remote communication link information that may be display a suggested sample location, a suggested sample drawer location, a suggested stainer location, or the like. From this the user may be able to accept a proposed action and may even be able to accept or reject the suggestion and communicate that decision over a remote, continuous, or perhaps transient link. Naturally, such activities as well as any rescheduling or simulating may be the result of an operator request also communicated over the link or network.
Similar to the act of suggesting to the operator a particular action that may enhance scheduling, the system may act to communicate over the link or network to inform the operator of needed events or the like. If a particular substance is required but is not present in the machine (likely as sensed by the device itself perhaps through the optical sensor), the system may automatically prompt an operator for a particular action needed, such as insert the needed reagent or the like. In downtime or otherwise, the system may even repetitively automatically check if an operator action is needed. As such the system may include an automatic operator need prompt 608. It may also provide a variety of information such as real time status information, pending sample information, a real time completion estimate for an aspect (e.g., a sample, a drawer, a batch, or the like). Each of these may be accomplished by software and hardware perhaps by including a real time status information element, a pending sample information element, or a real time completion estimate element, each shown conceptually as the information element 609.
As to any of the above capabilities, such may not only act independent of the automated process operation capabilities, but where applicable, they may be fully functional even without the presence or operability of the automated process operation capability (which itself may or may not be in a process device). They may be achieved in a variety of manners, including by providing a separate full function computer 181 (e.g., separate from the capability provided or required by a process system) that may be programmed to accomplish the desired function. In addition, in order to accomplish a goal of addressing practical and institutional needs, any capability may be configured to provide simplified use and may even be available in a highly simplified level of detail. This may be a “wizard” type of system where there is a “step-by-step” method for functions such as adding slides, achieving the desired input, or the like. Such an aspect may even be simple, regimented, and somewhat inflexible. A structured or simplified input can facilitate input by persons not required to have the full spectrum of skills necessary to be responsible for the operation of the sample processing system 101.
As part of the functions of monitoring or perhaps providing historical information, or even a play back of events, the system may include some type of data capture element 414. As may be appreciated from the initial discussion of the types of actions potentially needing to be programmed, the data capture element 414 may capture individual movement data, only robotic action data, individual robotic movement data, individual operation data, or even individual usage data. Thus the data capture element 414 may be an individual movement data capture element, a robotic action data capture element an individual robotic movement data capture element, or an individual operation data capture element. All or any part of this data may be systematically stored such as storing all important details, only particularly important details (e.g., relative to highly sensitive valves, substances, or the like) or even only a significant number of details relative to sample process operations. Thus the data capture element 414 may be a systematic process detail capture element. Once captured, this data may be stored in a number of perhaps redundant fashions as discussed above.
In storing the data, the system may create a segmented computer file, that is a file that contains only such data so that it is not as manipulatable as other files. This may aid in assuring the accuracy or even certifiability of the events depicted. For instance for any particular sample, there may be automatically generated upon request a simulation—perhaps with a time base appended—of what happened to that particular sample as well as pictures of the sample before and after its processing. The data so stored may even be created as an inalterable computer record and perhaps may even include an integral change indicia that can prove its accuracy. When stored, the system may create a common format computer record so that user can easily work with it or it may create a proprietary format computer record that cannot be altered or the like. Thus the significant process detail memory 412 may represent a segmented computer file memory element, an inalterable computer record memory element, an integral change indicia memory element, a common format computer record memory element, or a proprietary format computer record memory element.
The capture of historical information may include time of occurrence data, such as actual date data, actual time data (e.g., UTC, etc.), precise time data (e.g., hours, minutes, seconds), relative time data, absolute time data, initiation time data, completion time data (e.g., process, protocol, motor operation events, or the like), reagent lot, and reagent expiration data. Again, the data capture element 414 may include, but is not limited to, a time of occurrence data capture element, an actual date data capture element, an actual time data capture element, a precise time data capture element, a relative time data capture element, an absolute time data capture element, an initiation time data capture element, or a completion time data capture element.
One item that may be of particular user desire is the fact that the data capture element 414 may represent an individual sample process data capture element, an individual slide log data capture element, a type of protocol data capture element, and even an individual slide log data capture element. There may also be a real time individual slide log data display to show actual processing as it occurs.
As used above, the slide identification information may represent any information unique to a particular slide, such as a serial number, patient number, patient name, unique image, or the like. In keeping with privacy concerns, there may also be coded or perhaps encrypted identification information or internal identification information that others cannot use to identify the particular patient involved or the like. As discussed below and as shown in FIGS. 8 & 9, the overall system may include a number of staining instruments and thus the input permitted to be communicated over the link or network can include preferred stainer information (which may or may not be indicated or accepted by the automated system). Provision can also be included to communicate a desire to conduct a rush or stat test when there is an immediate or urgent need for process information. Such may also be linked with user privileges information so that only certain individuals may displace other tests to create a different priority. Of course all permutations and combinations of the above may be included.
For automated operation, the input may create data such as parameter process data 174 that may be perhaps redundantly stored at some location(s). To provide autonomous operation, it may be independently stored on the processing system involved perhaps in the multiple memory elements 701. It may also be stored at a separate electronic location or on a physically independent memory remote from an actual stainer itself. This may be accomplished by utilizing the communication link or perhaps by using the network if provided. It may involve use of the primary or secondary storage perhaps of a separate full function computer programmed or configured to accept and/or store data. In such a fashion, the computer may contain what could be considered as an independent memory 174. Since the computer is likely physically separate, it may be considered to have a physically independent memory, a separate electronic location, or perhaps even a remote location memory such as when it is remote from the process equipment.
By using independent memory and independent other functionality, the system may facilitate full operational functionality of the automated process operation capability. Since the automated process operation capability is fully operational during operation of either the memory or input, the storing or inputting or other function can be conducted without interrupting the process operation. Thus the inputs can be later accessed at a process time independent of the time of accomplishing slide process parameter input or storing. In addition, entry or storing may also be accomplished at least in part concurrently with the processing of certain samples. This processing may even be initiated significantly after completion of the slide process parameter input action. Such may occur at least about one hour after the input, at least about three hours after the input, at least about eight hours after the input, at least about one day after the input, at least about two days after the input, and at least about one week after the input.
All this information must, of course be used by some person. Any interested person may have the information available to them, such as an operator (e.g., anyone responsible for all or a portion of a process or the instrument), an instrument operator (e.g., an individual physically responsible for all or a portion of a process), an administrator (e.g., a person managing operators or perhaps responsible for order placement), a substance or other supplier, or even a manufacturer, such as for support and maintenance capability. For events that may require external actions (e.g., ordering more reagent or the like), the system may automatically notify at least one of these types of people and thus the automatic notice element 404 (such as a display which may be visual or otherwise) may be considered as representing an automatic operator notice element, an automatic administrator notice element an automatic supplier notice element or an automatic manufacturer notice element. It may also be considered as representing an automatic operator exteriorly-consequential information notice element, an automatic administrator exteriorly-consequential information notice element an automatic supplier exteriorly-consequential information notice element or an automatic manufacturer exteriorly-consequential information notice element.
Notice may be given at a variety of times. The system may act to automatically advance notify a person such as of an upcoming expiration date or of a need to reorder in advance. In so doing it may have or have input to it some type of lead time information that tells it how early to take the action. By properly configuring a lead time information data element lead time may vary by location and situation, for example a machine around the world or used continuously for critical processing may have a longer lead time than a machine right next to a supplier or used only sporadically. Order lead time information, reagent order lead time information, maintenance lead time information (any of which may vary over the course of a year or from time to time) may be utilized and as such the lead time information data element may represent an order lead time information data element, a reagent order lead time information data element, or a maintenance lead time information data element.
Communication, such as a notice or the like, may be displayed in a variety of ways. Internet and other links can be established so that an operator need not be physically attending to the sample process system while interacting with it. The system may be designed to respond to a remote information link 711 such as shown in FIG. 10 where the link is provided through the separate full function computer 181. As mentioned above, this interaction may be repetitive, continuous, or transient such as when including a transient remote response functionality. Through the communication link(s) available to it, the system may even automatically E-mail a person through inclusion of an E-mail notice element; it may automatically print out (including faxing) a notice by having an automatic printout notice element. Among other possibilities, it may automatically utilize a telephone line for simulated or reproduced voice or other information, may have an automatic telephone line utilization element, may have automatic internet communication capabilities, may have TCPIP capabilities, or the like.
In some embodiments, the system may be comprised of independent or perhaps redundant slide staining modules (some embodiments may comprise eight modules) as shown for some embodiments in FIGS. 1 and 6. Throughput may be based on the time to first result with the system allowing access to completed slides as soon as a staining module has completed the scheduled staining tasks. The multiple independent or redundant staining modules may allow for both continuous and batch processing of slides. Additionally, each independent staining module may also allow for the independent pre-treatment and staining of each slide. A carrier retainment assembly, such as a slide retainment assembly, may be used to introduce slides to be processed into the drawer 104, the drawer, slide retainment assembly, and components thereof forming a stain module. The slides may occupy one or more positions of the slide retainment assembly, such as at carrier retention devices, up to the capacity of the slide retainment assembly with the potential for each slide being processed independently of other slides configured with the slide rack. Embodiments of the stain modules, drawers, slide racks, and components thereof are also shown in FIG. 6. FIG. 6 also provides other embodiments of system features, such as an embodiment of the arm 120 and the component features of the arm.
Slide retainment assemblies having one or more slides and even reagent containers may be introduced into the staining or reagent modules by introduction into drawers 104 one at a time or in any combination until all or an appropriate number of staining modules are appropriately occupied. There may be no restrictions as to the order, number or timing of when the slide retainment assemblies are introduced into the system, the system may also allow for adaptive scheduling of sample loading. Staining modules, and in some embodiments the drawers of the staining modules, may lock out access to the slides during the processing period and may release them to the operator upon completion of the staining or other process on the last slide of that module. In some embodiments, the order in which the slide retainment assemblies are released may be dependant on the time required to process the last slide of the retainment assembly. Slides may even be processed in the most time efficient manner independently of the order to which they were introduced into the system. The system may provide an optimum or merely an enhanced temporal scheduling of the various sample process steps. To accomplish this, the system may automatically schedule steps that are interspersed for an enhanced time result. This interspersing may be an interleaving of a number of process operations and even an interleaving of a number of individual sample operations. In addition to interleaving steps, the system may sequence the individual sample operations. Regardless as to how programmed, it may be configured through hardware or software or a combination of each to provide an enhanced temporal scheduler element 179, a process operations interleave element, an individual sample operations interleave element, or even an individual sample operations sequence element. These can be created by integrating the automated process operation capability and either the parameter data or perhaps some replicated portion of that parameter process data (as mentioned later) and can thus act to create an interspersial robotic control functionality.
The control of the processing samples may be accomplished according to the following preferred embodiments, one preferred embodiment shown in FIG. 5, although other processing may be accomplished consistent with the present invention.
The processing sequence may be input, such that the various steps of a protocol for samples may be automated by one or more algorithmic controls. Input may be accomplished as follows: 1) selecting a first protocol step, 2) selecting a second protocol from a restricted list of menu items that are compatible with the first protocol step, and 3) selecting subsequent protocol steps from a restricted list of menu items that are compatible with the preceding protocol step.
As shown in FIGS. 8 & 9, in expanded systems, a sample processing system manager, such as a computer server may be connected with a number of individual sample processing systems. These may represent automated slide stainers or even stand alone automated slide processing systems such that they are fully capable of functioning with connection to other devices. In systems where a connection does exist, the capability of electronically connecting a number of automated slide stainers or automated sample processing systems or printers 200, may be provided. As mentioned earlier, there may be one or more separate full function computers connected. The connection may be established as a connection to a physically separate system such as the separate full function computer 181. Connection may be through a hub 193. There may be a multitasked central processing unit resource on either the stainer or the computer or there may be a number of central processing units that are configured to avoid using or implementing a multitasked central processing unit resource relative to the process operations in order to maintain full independence or perhaps even autonomous operation. The connection, whether for input or other operation may also be a remote link (including ability to be made remote such as in detachable memory) such as an Internet connection element a telephone line connection element, a wireless communication element a hardwired connection, or even a detachable memory element. In a preferred embodiment, connection among perhaps a number of process systems and perhaps a number of computers, such as workstations and a server (the latter residing either separately or as part of a workstation), may be achieved by use of a local area network (LAN), such as a group of computers and associated devices that share a common communications line or perhaps wireless link and may even share the resources of a single processor, memory, or server within a small geographic area (for example, within an office building or complex). A local area network for this type of system may also include features such as but not limited to: an Ethernet element, a token ring element, an arcnet element a fiber distributed data interface element, an industry specification protocol, a bluetooth-based element (named but not contemporary to King Harald Bluetooth of Denmark in the mid-tenth century!), a telecommunications industry specification using a frequency band of 2.45 GHz, a communication specification applying an IEEE 802 standard, a frequency hop communication specification, a shared common link element, a transmission control protocol/internet protocol communication element, a packetized information protocol, a shared protocol, a proprietary protocol, and even a layered protocol exchange system. By providing an electronic connection 176 between various resources, the local area network such as the stainer network 183 (a network dedicated to only the stainer or perhaps sample processing resources for integrity, security, and other purposes) in one embodiment may transmit a electronic memory address to achieve access to the appropriate information. Connection may also be established to an external network, an office network, a laboratory network, facilities intranet system, or even a lab information system 195 (LIS) such as through a bridge 194.
As mentioned, connection may be accomplished over Internet connections but more preferably is accomplished over local area network connections that are isolated from other communication traffic or instructions so that integrity of the processing events and system can be assured. Thus using a separate stainer network 184 may permit for an isolation functionality or an isolated electrical connection. Bridge 194 may be included in such a design. In addition, each sample processing system may be individually controlled, in some embodiments, by a PC attached with, internal to, or otherwise provided. Data sharing between sample processing systems and a system manager may be performed to allow identification, tracking, and status of sample batches, reagents, and other agents and components of the sample processing system. A determination of which system has which reagents, reagent type, slides and protocols may be performed. Log files for each processing sequence, protocol, or slide can be generated for monitoring processing status. Database maintenance (including but not limited to purge, compact, back-up, archive, database/list functions) and system diagnostics (including but not limited to exercising active system components to verify proper operation and assisting in troubleshooting efforts) may be accomplished manually or automatically and may be communicated over the various link(s) available.
In a networked embodiment or otherwise, the system may be configured to automatically access the required data through operation of the process operation control system 171 by inclusion of an automatic memory access element. This access may be achieved by specifying an electronic memory address that may be transmitted by a electronic memory address element 178 perhaps over an isolated local area network and may be followed by automatically replicating that data on some a memory aspect appropriate for operation such as an automatic data replication memory.
In a network embodiment, a sample processing system manager, such as a computer server or manager 500 may be connected with individual sample processing systems. This may be accomplished over Internet connections but more preferably is accomplished over LAN connections. Each sample processing system may be individually controlled, in some embodiments, by a PC or a separate full function computer 181 attached with, internal to, or otherwise provided. Data sharing between sample processing systems and the system manager may be performed through the communication link(s) to allow identification, tracking, and status of sample batches, reagents, and other agents and components of the sample processing system. A determination of which system has which reagents, reagent type, slides and protocols may be performed. Log files for each processing sequence, protocol, or slide can be generated for monitoring processing status. Database maintenance (including but not limited to purge, compact, back-up, archive, database/list functions) and system diagnostics (including but not limited to exercising active system components to verify proper operation and assisting in troubleshooting efforts) may be accomplished manually or automatically over the communication link(s) if and when available.
A control interface may be provided for the operator, such as a graphical user interface (GUI), and may accommodate various languages. Help menus may be provided to assist in sample processing. Password protection features can be provided and even administrator control over at least some aspects. This may include the capability to include administrator limitations on the functional availability of any aspect of the system or of specific stainer availability or functionality, certain reagent availability functionality, certain protocol availability functionality, patient identification information access functionality, process priority request functionality, and immediate, urgent, or stat process request functionality.
After all data is input, the system may act to determine operational readiness by inclusion of an operational readiness determination element 177 that may be programmed to assess if appropriate resources, drawers, slides, reagents, or other aspects are present or available to the system. As mentioned above it may communicate this information over the links or perhaps the network to an operator or other person.
Upon initial programming or when alteration of the aggregate event topology occurs, scheduling of events can occur. This may include consideration of timing tolerances, referred to in some embodiments as “bubble tolerance”, that may be controlled as between steps, such as between aspiration cycles. Additional control may be accomplished through timing algorithms to determine time tolerances of components of the processing system, such as the monitoring of “shelf life” or viability of reagents. Furthermore, adaptive scheduling of sample and slide insertion and removal into the system, as previously described, may be accommodated on an on-going basis throughout operation of the sample processing system.
One aspect of the invention focuses on an automated staining apparatus and a method of automated treating of samples. As to this aspect, the present invention relates to an automated staining apparatus for treating samples arranged on carrier elements or means, such as but not limited to microscope slides, located at defined positions close to or in the apparatus by removing a portion of selected reagent from a station containing a plurality of reagents and thereafter applying the reagent to a sample, e.g. a tissue, organic cells, bacteria etc., arranged on the carrier means. This aspect of the invention facilitates that two or more reagents are mixed and the mixture applied to a sample. It also relates to a method of automated treating of samples by mixing reagents and applying the mixture to the samples.
Staining apparatuses for staining and treating samples by means of a probe normally comprises a first station for containing one or more reagent containers; a second station for mounting slides, a probe arranged for removing a portion of reagent from a selected reagent container and applying the reagent to a slide on which the sample is arranged and a drive means for moving the probe between the various stations.
An object of this aspect of the present invention is to improve the known apparatuses for staining samples as well as the method for automatic staining of samples by facilitating a wider range of available processes or procedures used to implement treatment, so as to ease the implementation 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.
The term staining is used for the end product of the process, by which certain parts of the sample may be stained, i.e. has obtained 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 has to undergo a series of treatment steps, such as 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 may be 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 dissolved ratios. Some process steps require mixtures of two or more reagents that, when mixed, have a limited time window of usability because internal chemical processes deteriorate the mixture. By providing a staining 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 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.
The carrier elements or perhaps 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 situated in 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 staining apparatus may generally be controlled by means of a control element or perhaps a control means, typically a computer having a central processing unit and one or more memory units associated therewith, an control element or perhaps a means for controlling the various operations of the apparatus by controlling stepper 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 staining apparatus and connected to the apparatus via a data transmission port thereof.
The operation of the staining 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 the various operations of the apparatus by controlling stepper 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 internal, wire, or wireless elements. The control element or perhaps means does not have to be physically arranged within the apparatus itself but may be a computer external to the staining apparatus and connected to the apparatus via a data transmission port thereof.
The present invention also relates to a method of fully automated treating of samples arranged on carrier elements by means of a staining apparatus controlled by means of a control element or means, wherein the method comprises the steps of situating a plurality of carrier means intermediately in a carrier means station, each carrier means having a sample arranged thereon, applying a portion of a first reagent selected from a plurality of reagents to a mixing cup, applying 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, removing 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 applying the mixed reagents to the selected carrier means, so as to perform a treatment of the sample arranged on the selected carrier means.
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.
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.
As shown in FIG. 6, a detailed description of one embodiment of this aspect of the invention involves staining apparatus 201. The staining apparatus 201 may comprise a rectangular frame 204 surrounding a first station 202 comprising an array of compartments wherein each compartment a reagent container 203 is placed, and a second station 205 wherein a number of separate racks 206 is placed, and where each rack may comprise a number of slides 207 mounted side by side in the rack 206. A robot arm to move a probe 124 in X and Y direction may be arranged above the frame 204 of the staining apparatus. The robot arm may therefore position the probe 124 above all reagent containers 203 as well as above all the slides 207, and may further operate the probe 124 in the Z direction to remove portions of a reagent contained in any of the containers 203, to transfer the portion of reagent and apply it to any of the slides 207 in order to provide a selected staining or treatment of the sample on each slide 207. By use of a suitable control element, e.g. a computer having the appropriate software, subroutines, or input data for the purpose, this staining apparatus 201 may be able to automatically stain or treat samples requiring different staining or treatment reagents and processes.
Having the appropriate input data, the control element or perhaps means of the apparatus may operate the robot arm to commence a staining or treatment run by moving the probe to a first reagent container 203, into which the probe tip is inserted and liquid is aspirated up into the probe 124 in an amount corresponding to the number of samples to be stained or treated, in accordance with the input data provided to the control element Additionally, under certain conditions, the instrument may be required to perform a reagent inventory before a staining or treatment run can commence. This inventory may be accomplished by use of the probe tip to actually touch the liquid surface in each reagent vial 203. To prevent cross-contamination between the reagents in the various containers 203, a cleaning of the probe 124 or at least the probe tip may be required after each measurement of a reagent level.
The probe 124 may be moved by the robot arm towards the slide retainment assembly 205 in which the slides 207 are mounted. The slides 207 may be situated with the surface horizontally oriented and the probe 124 may dispense the required amount of reagent on the appropriate slides in accordance with the input data. Alternatively, the probe 124 may be moved by the robot arm towards the reagent mixer 209 where it may release reagent into the cup of the reagent mixer 209, and may be subsequently moved to the probe washing station 208. The robot arm may move the new clean probe to a second selected reagent container 203 for collecting a selected amount of reagent from the second vial 203, and the probe may thereafter by means of the robot arm be moved to the reagent mixer 209, where the reagent in the probe 124 may be released into the cup of the mixer containing the first selected reagent. This may be commenced several times if more than two reagents are to be mixed for a specific staining or treatment process.
An object of the present invention is to provide a staining apparatus and a method for automatic staining of samples, in which the total process time for completing or even entering the staining protocol may be reduced. In particular, it is an object of this aspect of the invention to reduce the amount of time needed in general.
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 sample processing techniques as well as various systems, assemblies, and devices to accomplish sample processing, input, and other functions. In this application, the sample processing techniques are also disclosed as part of the results shown to be achieved by the various systems, assemblies, and devices described and as steps which are inherent to utilization. They should be understood to be 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. Importantly, neither the description nor the terminology is intended to limit the scope of the claims which may be included at any time.
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 at any time.
Further, each of the various elements of the invention and claims may also be achieved in a variety of manners. 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 “retention element” should be understood to encompass disclosure of the act of “retaining”—whether explicitly discussed or not—and, conversely, were there effectively disclosure of the act of “retaining”, such a disclosure should be understood to encompass disclosure of a “retention element” and even a “means for retaining”. It should also be understood that in jurisdictions where specific language may be construed as limiting, as but one example in the United States where some interpretations of “means for” elements can be construed narrowly, broader equivalent language may be used and should be understood as encompassed by this specification. Such changes and alternative terms are to be understood to be explicitly included in the description.
Any patents, patent applications, 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 as well as the definitions presented by searchStorage.com, and the American National Standards Institute, Inc. American National Standard for Telecommunications, Telecom Glossary 2000 as also available at www.atis.org, such to be considered as representing the meaning of the terms as understood by computer professionals. Finally, the priority cases for this application is hereby appended and hereby incorporated by reference, with specific reference made to and specific incorporation by reference of the disclosures in five of assignee's other sample processor disclosures, namely:

    PCT/US03/040974 filed Dec. 19, 2003, listing DakoCytomation Denmark A/S as assignee and entitled “Information Notification Sample Processing System and Methods of Biological Slide Processing”;
    PCT/US03/040591 filed Dec. 19, 2003, listing Dakocytomation Denmark A/S as assignee and entitled “Enhanced Scheduling Sample Processing System and Methods of Biological Slide Processing”;
    PCT/US03/40519 filed Dec. 19, 2003, listing Dakocytomation Denmark A/S as assignee and entitled “Advance Programmed Sample Processing System and Methods of Biological Slide Processing”;
    PCT/US03/40518 filed Dec. 19, 2003, listing Dakocytomation Denmark A/S as assignee and entitled “A Method and Apparatus for Automatic Staining of Tissue Samples”; and
    PCT/US03/40880 filed Monday Dec. 22, 2003, listing Dakocytomation Denmark A/S as assignee and entitled “Systems and Methods of Sample Processing and Temperature Control”.


Thus, the applicant(s) should be understood to have support to claim at least: i) each of the sample processing systems and subsystems as herein disclosed and described, ii) the related methods disclosed and described, iii) similar, equivalent, and even implicit variations of each of these systems, assemblies, 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, and ix) methods and systems, assemblies, devices, and apparatuses substantially as described hereinbefore and with reference to any of the accompanying examples, x) the various combinations and permutations of each of the elements disclosed, xi) each potentially dependent claim or concept as a dependency on each and every one of the independent claims or concepts presented, xii) processes performed with the aid of or on a computer as described throughout the above discussion, xiii) a programmable system as described throughout the above discussion, xiv) a computer readable memory encoded with data to direct a computer comprising means or elements which function as described throughout the above discussion, xv) a computer configured as herein disclosed and described, xvi) individual or combined subroutines and programs as herein disclosed and described, xvii) the related methods disclosed and described, xviii) similar, equivalent, and even implicit variations of each of these systems and methods, xix) those alternative designs which accomplish each of the functions shown as are disclosed and described, xx) those alternative designs and methods which accomplish each of the functions shown as are implicit to accomplish that which is disclosed and described, xxi) each feature, component, and step shown as separate and independent inventions, and xxii) the various combinations and permutations of each of the above.
Further, if or when used, the use of the transitional phrase “comprising” or the like 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” or the like, 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.
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.

## Claims

1. A method for performing operations on a stainer in a stainer network comprising:
providing a robotic arm coupled to the stainer, the robotic arm having a reagent dispenser;
establishing a network connection between a computer and a stainer in the stainer network;
sending requests from the computer to the stainer over the network connection;
inserting a first sample into the stainer;
processing a first sample with the stainer using the requests received from the computer, wherein said processing comprises dispensing reagents to the sample with the reagent dispenser of the robotic arm; and
inserting a second sample into the stainer and at least one reagent into the stainer during the processing of the first sample without interrupting the dispensing of reagents onto the first sample with the reagent dispenser of the robotic arm.

2. The method of claim 1, wherein the computer is a server and wherein the stainer is a client of the server.

3. The method of claim 2, wherein the server includes a centralized database including configuration information for the stainer.

4. The method of claim 1, wherein the stainer network is connected to a laboratory information system.

5. The method of claim 4, further including sending requests from the laboratory information system to a server including a centralized database comprising information about the stainer, wherein the information includes status information on stainers, slides, consumables, and treatment protocols of the stainer.

6. The method of claim 5, wherein the requests from the laboratory information system to the server including the centralized database further comprise database maintenance operations including information purging, information compaction, and database information back-up operations.

7. The method of claim 3, further comprising:
sending a request from the computer to run diagnostic tests on the stainer,
storing diagnostic information in the centralized database,
retrieving the diagnostic information about the stainer from the centralized database by the computer; and
providing the diagnostic information to a user.

8. The method of claim 7, further comprising exercising active components of the stainer as a diagnostic test, the active components including at least one of the robotic arm, the reagent dispenser, an optical sensor, an actuator probe, and a non-discrete applicator.

9. The method of claim 8, further comprising electronically notifying an operator about the results of the diagnostic tests.

10. The method of claim 1, further comprising performing automatic diagnostic operations on the stainer while operating other stainers in the stainer network, wherein the operations of the other stainers are not materially affected by the operations of the stainer.

11. The method of claim 1, further comprising monitoring by the computer a status of at least one of the first sample or the second sample in the stainer.

12. The method of claim 1, further comprising providing by the computer a real-time estimate of a completion time of the first sample being processed by the stainer.

13. A method for performing operations on a stainer in a stainer network comprising:
providing a robotic arm coupled to the stainer, the robotic arm having a reagent dispenser;
establishing a network connection between a computer and a stainer in the stainer network;
sending requests from the computer to the stainer over the network connection;
sending requests from the laboratory information system to a server including a centralized database, wherein the centralized database contains status information chosen from slides on the stainer, amounts of consumables on the stainer or treatment protocols performed on the stainer;
inserting a first sample into the stainer;
processing a first sample with the stainer using the requests received from the computer, wherein said processing comprises dispensing reagents to the sample with the reagent dispenser of the robotic arm; and
inserting a second sample into the stainer and at least one reagent into the stainer during the processing of the first sample without interrupting the dispensing of reagents onto the first sample with the reagent dispenser of the robotic arm.

14. The method of claim 13, wherein the stainer network further includes a server and a plurality of stainers including the stainer, and wherein the stainer is a client of the server.

15. The method of claim 14, wherein the server includes a centralized database comprising configuration information for the stainer.

16. The method of claim 13, wherein the requests further comprise database maintenance operations including information purging, information compaction, and database information.

17. The method of claim 13, wherein the stainer is a first stainer,
the method further comprising:
sending requests from the computer to the stainer over the network connection according to an event topology;
providing a second stainer in the stainer network;
checking by the computer for operational readiness in the first stainer; and
altering the event topology according to the operational readiness.

18. The method of claim 17, further comprising:
sending requests from the computer to run diagnostic tests on the first or the second stainer,
storing diagnostic information in the centralized database,
retrieving diagnostic information about the first or the second stainer from the centralized database by the computer; and
providing the diagnostic information to a user.

19. The method of claim 18, further comprising exercising active components of the first or the second stainer as a diagnostic test, the active components including at least one of a robotic arm of the first or the second stainer, a reagent dispenser of the first or the second stainer, an optical sensor of the first or the second stainer, an actuator probe of the first or the second stainer, and a non-discrete applicator of the first or the second stainer.

20. The method of claim 19, further comprising electronically notifying an operator about the results of the diagnostic tests.

21. The method of claim 13, wherein the stainer is configured to be controlled from a remote location.

22. The method of claim 13, further comprising performing automatic diagnostic operations on the stainer while operating other stainers in the stainer network, wherein the operations of the other stainers are not materially affected by the operations of the stainer.

23. The method of claim 13, further comprising monitoring by the computer the status of at least one of the first sample or the second sample in the stainer.

24. The method of claim 13, further comprising providing by the computer a real-time estimate of the completion time of the first sample being processed by the stainer.