Abstract: A tangible computer-readable storage device storing computer-executable program instructions that generate a user interface for displaying workflow information associated with a tissue specimen in a pathology laboratory. The program instructions may be configured to perform a method including displaying a virtual laboratory component representing a physical pathology laboratory having one or more laboratory stations for processing the tissue specimen, wherein the tissue specimen is processed by the one or more laboratory stations according to a workflow, and displaying a specimen indicator that indicates a current specimen state based on a current relationship of the tissue specimen to the workflow.

Abstract: The present invention relates to compounds which are conjugates of two or more moieties capable of serving as substrates of an enzyme with peroxidase activity and one or more labels. The conjugate molecules of the invention are useful for detection of molecular targets, e.g. biological or chemical molecules, molecular structures, etc, in samples using a host of experimental schemes for detecting and visualizing such targets, e.g. immunohistochemistry (IHC), in situ hybridization (ISH), ELISA, Southern, Northern, and Western blotting, etc. The invention also relates to compositions comprising the conjugate molecules.

Abstract: Systems, methods, and apparatus are described for the handling of biological specimens for analysis. The systems, methods and apparatus are designed to reduce errors in misidentification, incorrect processing, and recordkeeping and reporting. The systems, methods, and apparatus can also provide real time tracking of samples at any stage, from collection to processing to analyzing to storage.

Abstract: Systems, methods, and apparatus are described for the handling of biological specimens for analysis. The systems, methods and apparatus are designed to reduce errors in misidentification, incorrect processing, and recordkeeping and reporting. The systems, methods, and apparatus can also provide real time tracking of samples at any stage, from collection to processing to analyzing to storage.

Abstract: Methods and systems for image scoring and analysis are provided. Scored and analyzed images may include digital pathology images. Image scoring and analysis methods may include techniques to identify nuclei and determine membrane staining extent through the use of a priori models. Image scoring and analysis methods may include techniques for membrane intensity determination. Images may be scored based on an extent of membrane staining and membrane intensity.

Abstract: The present invention concerns monomeric or polymeric linker molecules useful in biological and chemical applications, their synthesis, and the synthesis and use of derivatives of the linkers conjugated to a variety of detectable labels and other substances. The linkers may be used, for example, in conjunction with fluorescent labels, nucleic acid or nucleic acid analog probes, and solid phase systems, and to enhance the solubility of the conjugated molecules.

Abstract: The present invention concerns an apparatus for staining tissue samples, said apparatus including a reagent section or reagent containers; at least one staining section or tissue samples, a robotic head or robotic element that may move reagent to a predetermined tissue sample, said robotic element being moveable above the reagent and the staining sections, a control element that may manage a staining process, a 2-D optical sensor to detect two-dimensional image data of a relevant property and that can feed the captured image data to the control element. By providing the robotic element with a 2-D optical sensor, a common image processor may be provided having multiple functions. By using a 2-D optical image processing system, the control system of the apparatus may easily be adapted to read various types of data presentations, just as actual images for sections of the apparatus may be identified in order to assess the condition of the apparatus.

Abstract: The invention provides compositions and methods for the detection of targets in a sample; in particular, an in situ hybridization (ISH) sample. Probes and detectable labels may be provided in multiple layers in order to increase the flexibility of a detection system, and to allow for amplification to enhance the signal from a target. The layers may be created by incorporating probes and detectable labels into larger molecular units that interact through nucleic acids base-pairing, including peptide-nucleic acid (PNA) base-pairing. Optional non-natural bases allow for degenerate base pairing schemes. The compositions and methods are also compatible with immunohistochemistry (IHC), immunocytochemistry (ICC), flow cytometry, enzyme immuno-assays (EIA), enzyme linked immuno-assays (ELISA), blotting methods (e.g. Western, Southern, and Northern), labeling inside electrophoresis systems or on surfaces or arrays, and precipitation, among other general detection assay formats.

Abstract: The invention provides methods and compositions for performing a stringent wash step in a hybridization assay between at least one molecule and a target. The invention may, for example, eliminate the use of, or reduce the dependence on formamide in the stringent wash step. Compositions for use in the invention include an aqueous composition comprising at least one polar aprotic solvent in an amount effective to denature non-complementary sequences in a hybridization product.

Abstract: The present invention relates to a method of biological labeling that occurs via a free radical chain reaction. The labeling occurs due to deposition of a detectable reporter molecule from a media comprising a substance comprising at least two moieties of a peroxidase enzyme substrate (termed herein ‘cross-linker’) in a target site comprising peroxidase activity and a biological marker. The labeling reaction described herein may generally be used to detect targets in a host of experimental schemes for detecting and visualizing a biological or chemical target, including immunohistochemistry (IHC), in situ hybridization (ISH), antibody-based staining methods such as ELISA, Southern, Northern, and Western blotting, and others.

Abstract: The present invention relates to methods and compounds for enzyme-mediated amplification of target-associated signals for visualization of biological or chemical targets in samples, wherein the targets are immobilized, in particular the invention relates to the oxidoreductase-mediated signal amplification for visualization of targets in samples comprising cells. The methods of the invention are particular useful for qualitative and quantitative evaluation of biological markers relating to medical diagnostic and therapy.

Abstract: The invention provides compositions and methods for the detection of targets in a sample; in particular, an immunohistochemistry (IHC) sample. Probes and detectable labels may be provided in multiple layers in order to increase the flexibility of a detection system, and to allow for amplification to enhance the signal from a target. The layers may be created by incorporating probes and detectable labels into larger molecular units that interact through nucleic acids base-pairing, including peptide-nucleic acid (PNA) base-pairing. Optional non-natural bases allow for degenerate base pairing schemes. The compositions and methods are compatible with immunohistochemistry (IHC), but also could be used in immunocytochemistry (ICC), in situ hybridization (ISH), flow cytometry, enzyme immuno-assays (EIA), enzyme linked immuno-assays (ELISA), blotting methods (e.g.

Abstract: The invention provides methods and compositions for separately denaturing a probe and target in hybridization applications. The invention may, for example, eliminate the use of, or reduce the dependence on formamide in hybridization applications. Compositions for use in the invention include an aqueous composition comprising at least one polar aprotic solvent in an amount effective to denature double-stranded nucleotide sequences.

Abstract: The invention provides methods and compositions for hybridizing at least one molecule to an RNA target. The invention may, for example, eliminate the use of, or reduce the dependence on formamide in RNA hybridization applications. Compositions for use in the invention include an aqueous composition comprising at least one nucleic acid sequence and at least one polar aprotic solvent in an amount effective to enable hybridization to RNA.

Abstract: The present invention provides compositions and methods for the detection of nucleic acid sequences associated with chromosomal aberrations. The invention may, for example, eliminate the use of or reduce the dependence on formamide in hybridization. Compositions for use in the invention include an aqueous composition comprising at least one nucleic acid sequence and at least one polar aprotic solvent in an amount effective to denature double-stranded nucleotide sequences.

Abstract: An apparatus (100) for processing a biological sample (101). The biological sample being arranged on a first planar surface (102) of a carrier (103). The apparatus comprises a second planar surface (104) arranged substantially parallel to said first planar surface and at a first distance from said first planar surface, said second planar surface are arranged at an angle (A) greater than zero degree from the horizontal plane (HP); supply means (126, 131, 220) for supplying an amount (105) of a liquid that is to be applied to said biological sample. The first planar surface and the second planar surface are configured to be arranged in a second distance from each other, said second distance being such that said supplied amount of liquid is distributed over said biological sample when said first planar surface and second planar surface are brought to said second distance from each other.

Abstract: A sample processing system that may be automated and methods are disclosed where samples are arranged on a carrier element and a process operation control system automatically processes the samples perhaps robotically with an operationally-influential exteriorly-consequential information monitor or a data capture element. Significant process details as well as operationally-influential exteriorly-consequential information may be monitored and an automatic notice element may cause notification of a person at some display that may be remote. Various people may be notified, such as an administrator, a supplier, or a manufacturer of an opportunity for some action such as reagent reordering or the like. A simulated motion display may be included to “watch” simulated operation in real time or long after completion of the actual processing.

Abstract: Methods and systems for image scoring and analysis are provided. Scored and analyzed images may include digital pathology images. Image scoring and analysis methods may include techniques to identify nuclei and determine membrane staining extent through the use of a priori models. Image scoring and analysis methods may include techniques for membrane intensity determination. Images may be scored based on an extent of membrane staining and membrane intensity.

Abstract: An apparatus for processing a biological sample is provided. The biological sample being arranged on a first planar surface of a carrier, the apparatus having a second planar surface arranged substantially parallel to said first planar surface and at a first distance from said first planar surface. The first planar surface and said second planar surface are arranged at an angle (A) greater than zero degree from the horizontal plane (HP). The apparatus having a supply for supplying an amount of a liquid that is to be applied to said biological sample. The first planar surface and said second planar surface are configured to be arranged at a second distance from each other, said second distance being such that said supplied amount of liquid is distributed over said biological sample when said first planar surface and said second planar surface are brought to said second distance from each other.

Abstract: Systems and methods in accordance with embodiments of the present invention allow for the automatic control and scheduling of a staining apparatus for biological samples on slides present within the apparatus. In some embodiments, the actions of a robot coupled to the staining apparatus, which performs some of the staining tasks on the individual slides in accordance with their respective protocols, may be prioritized and scheduled. In some embodiments, the scheduling may result in increasing or maximizing the throughput of slides. In some embodiments, robot scheduling ensures that the individual slides are processed substantially within the tolerances specified by their respective protocols. In some embodiments, the robot scheduler may respond to spontaneous user actions and adaptively schedule or re-schedule robot actions.