Abstract: A system and method of displaying of multiple simultaneous views of a same region of a biological tissue sample. Logical instructions are executed by a processor to perform operations such as receiving a plurality of images of the biological tissue sample, converting the plurality of images to a common reference frame based on the individual metadata of each image, and arranging the plurality of images into a display pattern for simultaneous viewing of different aspects of the imaged biological tissue sample on a display screen. The plurality of images is produced by preprocessing images of the biological tissue sample. Each image shows a view mode of a same region of the biological tissue sample, and each image contains metadata that describe spatial orientation, such as the translation, rotation, and magnification, of the image to bring the plurality of images to a common view.

Abstract: This disclosure describes methods, kits, and systems for scoring the immune response to cancer through examination of tissue infiltrating lymphocytes (TILs). Methods of scoring the immune response in cancer using tissue infiltrating lymphocytes include detecting CD3, CD8, CD20, and FoxP3 within the sample and scoring the detection manually or scoring the digital images of the staining with the aid of image analysis and algorithms.

Abstract: This disclosure describes methods, kits, and systems for scoring the immune response to cancer through examination of tissue infiltrating lymphocytes (TILs). Methods of scoring the immune response in cancer using tissue infiltrating lymphocytes include detecting CD3, CD8, CD20, and FoxP3 within the sample and scoring the detection manually or scoring the digital images of the staining with the aid of image analysis and algorithms.

Abstract: Described herein are methods for co-expression analysis of multiple markers in a tissue sample comprising: computing a heat map of marker expression for each of a plurality of single marker channel images, wherein each of the plurality of single marker channel images comprise a single marker; identifying one or more candidate regions of interest in each heat map of marker expression; computing overlay masks comprising the identified one or more candidate regions of interest from each heat map of marker expression; determining one or more co-localized regions of interest from the overlay masks; mapping the one or more co-localized regions of interest to a same coordinate position in each of the plurality of single marker channel images; and estimating a number of cells in at least one of the determined one or more co-localized regions of interest in each of the plurality of single marker channel images.

Abstract: A system and method of displaying of multiple simultaneous views of a same region of a biological tissue sample. Logical instructions are executed by a processor to perform operations such as receiving a plurality of images of the biological tissue sample, converting the plurality of images to a common reference frame based on the individual metadata of each image, and arranging the plurality of images into a display pattern for simultaneous viewing of different aspects of the imaged biological tissue sample on a display screen. The plurality of images is produced by preprocessing images of the biological tissue sample. Each image shows a view mode of a same region of the biological tissue sample, and each image contains metadata that describe spatial orientation, such as the translation, rotation, and magnification, of the image to bring the plurality of images to a common view.

Abstract: A system and method of displaying of multiple simultaneous views of a same region of a biological tissue sample. Logical instructions are executed by a processor to perform operations such as receiving a plurality of images of the biological tissue sample, converting the plurality of images to a common reference frame based on the individual metadata of each image, and arranging the plurality of images into a display pattern for simultaneous viewing of different aspects of the imaged biological tissue sample on a display screen. The plurality of images is produced by preprocessing images of the biological tissue sample. Each image shows a view mode of a same region of the biological tissue sample, and each image contains metadata that describe spatial orientation, such as the translation, rotation, and magnification, of the image to bring the plurality of images to a common view.

Abstract: Systems and methods for automatic FOV selection in immunoscore computation that involve reading images for individual markers from an unmixed multiplex slide or single stain slides, and computing the tissue region mask from the individual marker image. The heat map of each marker is determined by applying the low pass filter on the individual marker image channel and selecting the top K highest intensity regions from the heat map as the candidate FOVs for each marker. The candidate FOVs from the individual marker images are merged together in the same coordinate system by either adding all of the FOVs together or by only adding the FOVs from the selected marker images depending on the user's choice, and registering all the individual marker images to a common coordinate system and transferring the FOVs back to the original images.

Abstract: Embodiments disclosed herein are directed, among other things, to imaging systems, methods, and apparatuses for automatically identifying fields of view (FOVs) for regions in an image encompassing tumor are disclosed. In embodiments and in further aspects of the present invention, a computer-implemented method is disclosed for a tumor region based immune score computation. The method, in accordance with the present invention, involves identifying regions, for example, tumor areas or regions around a tumor area, partitioning a whole slide image or portion of a whole slide image into multiple regions related to the tumor, selecting FOVs within each identified region, and computing a number of cells present in each FOV. An immune score and/or immune-related score may be generated based on the cells counted in each FOV.

Abstract: A system and method of displaying of multiple simultaneous views of a same region of a biological tissue sample. Logical instructions are executed by a processor to perform operations such as receiving a plurality of images of the biological tissue sample, converting the plurality of images to a common reference frame based on the individual metadata of each image, and arranging the plurality of images into a display pattern for simultaneous viewing of different aspects of the imaged biological tissue sample on a display screen. The plurality of images is produced by preprocessing images of the biological tissue sample. Each image shows a view mode of a same region of the biological tissue sample, and each image contains metadata that describe spatial orientation, such as the translation, rotation, and magnification, of the image to bring the plurality of images to a common view.

Abstract: The present disclosure relates to materials and methods for evaluating prostate cancer using binding entities (such as antibodies) that bind to the N-terminus and the C-Terminus of androgen receptor. Prostate samples are histochemically labeled for the N-terminus and the C-Terminus of androgen receptor, and a ratio between the binding of the N- and C-terminal antibodies is determined.

Abstract: Described herein are methods for co-expression analysis of multiple markers in a tissue sample comprising: computing a heat map of marker expression for each of a plurality of single marker channel images, wherein each of the plurality of single marker channel images comprise a single marker; identifying one or more candidate regions of interest in each heat map of marker expression; computing overlay masks comprising the identified one or more candidate regions of interest from each heat map of marker expression; determining one or more co-localized regions of interest from the overlay masks; mapping the one or more co-localized regions of interest to a same coordinate position in each of the plurality of single marker channel images; and estimating a number of cells in at least one of the determined one or more co-localized regions of interest in each of the plurality of single marker channel images.

Abstract: Embodiments disclosed herein are directed, among other things, to imaging systems, methods, and apparatuses for automatically identifying fields of view (FOVs) for regions in an image encompassing tumor are disclosed. In embodiments and in further aspects of the present invention, a computer-implemented method is disclosed for a tumor region based immune score computation. The method, in accordance with the present invention, involves identifying regions, for example, tumor areas or regions around a tumor area, partitioning a whole slide image or portion of a whole slide image into multiple regions related to the tumor, selecting FOVs within each identified region, and computing a number of cells present in each FOV. An immune score and/or immune-related score may be generated based on the cells counted in each FOV.

Abstract: Disclosed herein are multiplex methods for co-detecting a B cell marker, TP53 nucleic acid, and Chromosome 17 centromere DNA in a single sample. Samples stained for the B cell marker (e.g., CD79a protein), TP53 nucleic acid, and Chromosome 17 centromere DNA may allow for the identification of the subtype of chronic lymphocytic leukemia (CLL) with the 17p deletion. The methods feature staining the B cell marker (e.g., CD79a) a first distinct color, TP53 in a second distinct color, and chromosome 17 centromere DNA in a third distinct color. Further disclosed are nucleic acid probes specific for 19q12, INSR, ATM, DLEU2, TP53, and 13q12.

Abstract: Systems and methods for automatic FOV selection in immunoscore computation that involve reading images for individual markers from an unmixed multiplex slide or single stain slides, and computing the tissue region mask from the individual marker image. The heat map of each marker is determined by applying the low pass filter on the individual marker image channel and selecting the top K highest intensity regions from the heat map as the candidate FOVs for each marker. The candidate FOVs from the individual marker images are merged together in the same coordinate system by either adding all of the FOVs together or by only adding the FOVs from the selected marker images depending on the user's choice, and registering all the individual marker images to a common coordinate system and transferring the FOVs back to the original images.

Abstract: This disclosure describes methods, kits, and systems for scoring the immune response to cancer through examination of tissue infiltrating lymphocytes (TILs). Methods of scoring the immune response in cancer using tissue infiltrating lymphocytes include detecting CD3, CD8, CD20, and FoxP3 within the sample and scoring the detection manually or scoring the digital images of the staining with the aid of image analysis and algorithms.