Abstract: The subject disclosure presents systems and methods for improved meso-dissection of biological specimens and tissue slides including importing one or more reference slides with annotations, using inter-marker registration algorithms to automatically map the annotations to an image of a milling slide, and dissecting the annotated tissue from the selected regions in the milling slide for analysis, while concurrently tracking the data and analysis using unique identifiers such as bar codes.

Abstract: An informatics platform provides an architecture to integrate information from relevant patient information systems.

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: The subject disclosure provides systems, computer-implemented methods, and clinical workflows for meso-dissection of biological specimens and tissue slides by incorporating annotation and inter-marker registration modules within digital pathology imaging and meso-dissection (or milling) systems. Images of a reference slide a milling slide may be acquired using the same imaging system, with the annotations on the image associated with the milling slide being based on the inter-marker registration. Each image along with its respective annotations and meta-data may be associated with a project or a case, and stored in an image management system. A same-marker registration may be used to map annotations from the annotated image of the milling slide to a live image of the milling slide. The milling slide may be milled based on the annotations, with milled tissue output into a contained that is labeled in association with the labeled input slides.

Abstract: Methods, systems, and apparatuses for detecting and describing heterogeneity in a cell sample are disclosed herein. A plurality of fields of view (FOV) are generated for one or more areas of interest (AOI) within an image of the cell sample are generated. Hyperspectral or multispectral data from each FOV is organized into an image stack containing one or more z-layers, with each z-layer containing intensity data for a single marker at each pixel in the FOV. A cluster analysis is applied to the image stacks, wherein the clustering algorithm groups pixels having a similar ratio of detectable marker intensity across layers of the z-axis, thereby generating a plurality of clusters having similar expression patterns.

Abstract: The present disclosure provides a method for processing at least one image comprising inputting the image to at least one neural network, the at least one network being configured to deliver, for each pixel of a group of pixels belonging to an object of a given type visible on the image, an estimation of object parameters that are parameters of the object. The method further comprising processing the estimations of the object parameters using an instance segmentation mask identifying instances of objects having the given type.

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: Methods, systems, and apparatuses for detecting and describing heterogeneity in a cell sample are disclosed herein. A plurality of fields of view (FOV) are generated for one or more areas of interest (AOI) within an image of the cell sample are generated. Hyperspectral or multispectral data from each FOV is organized into an image stack containing one or more z-layers, with each z-layer containing intensity data for a single marker at each pixel in the FOV. A cluster analysis is applied to the image stacks, wherein the clustering algorithm groups pixels having a similar ratio of detectable marker intensity across layers of the z-axis, thereby generating a plurality of clusters having similar expression patterns.

Abstract: Under one aspect, a method of displaying medical information about a subject having a plurality of regions includes: resolving light obtained from each region of the plurality of regions into a corresponding spectrum; selecting a portion of each spectrum, the selected portion including medical information about the corresponding region; constructing an image based on the selected portion of each spectrum; and projecting the image onto the subject. Under another aspect, a method of displaying medical information about a subject that has a plurality of regions includes: resolving light obtained from each region of the plurality of regions into a corresponding spectrum; selecting a portion of each spectrum, the selected portion including medical information about the corresponding region; constructing a spectral image based on the selected portion of each spectrum; displaying an image of the plurality of regions; and displaying the spectral image overlying the image of the plurality of regions.

Abstract: A digital pathology system and associated method and computer program product provide a quantitative analysis of entire tissue slides as well as intuitive, effective, fast, and precise quantification of biomarker expressions across relevant areas of the entire tissue slides. The digital pathology system enables a novel workflow that allows the user to efficiently outline clinically relevant morphology in its entirety, including solid tumor areas. Quantitative analysis results are then efficiently and intuitively provided to the user for all tissue content (i.e., millions of cells) within seconds. This efficiency is made possible by a pre-computation step that computes and stores image analysis results for later retrieval. Visualizing vast amount of data effectively is another component of the system that provides information and confidence to the user about the biomarker expression levels.

Abstract: An informatics platform provides an architecture to integrate information from relevant patient information systems.

Abstract: Methods and systems for generating a heat map that reduces bias in selecting FOVs are disclosed. Some disclosed methods include annotating a primary stained image, registering the annotation to a secondary serial specific stained image, using an image analysis algorithm to compute a scoring criteria specific to the tissue and assay type for tiled regions in the image, using a sliding window in the annotated tumor region to compute values for each pixel in a heat map which correlate to the specific scoring criteria, displaying the heat map at low resolution, ranking and selecting hot spots, selecting FOVs from the hot spot regions which results in displaying the slide-level score for the FOVs. The systems comprise, among other things, software configured to perform the referenced method.

Abstract: Provided are systems and methods for imaging with compensation functions. An imaging device comprises a plurality of light source sets, of which two or more light source sets emit light of a same specific spectral range to compensate intensity differences among different spectral ranges. The imaging device can be integrated with a mobile device. A method comprises a subtraction procedure to compensate ambient light effect, a normalization procedure to compensate incidence angle effect, a 3D reconstruction procedure to compensate distance effect, or any combination of these procedures. The method is performed at an imaging device comprising a controller. At least one program is non-transiently stored in the controller and executable by the controller.

Abstract: The subject disclosure presents systems and methods for improved meso-dissection of biological specimens and tissue slides including importing one or more reference slides with annotations, using inter-marker registration algorithms to automatically map the annotations to an image of a milling slide, and dissecting the annotated tissue from the selected regions in the milling slide for analysis, while concurrently tracking the data and analysis using unique identifiers such as bar codes.

Abstract: Automated systems and methods are presented for retrospectively analyzing clinical trial data. A plurality of image derived from biological samples of patients in a cohort population are accessed. Image features are computed based on the plurality of images. A diagnostic feature metric is derived based on the computed image features. A cut point value is determined by applying a statistical minimization method using the derived diagnostic feature metric and patient outcome data from the cohort population, in which the cut point value identifies a patient in the cohort population as positive or negative for a diagnostic test.

Abstract: Automated systems and methods for determining the variability between derived expression scores for a series of biomarkers between different identified cell clusters in a whole slide image are presented. The variability between derived expression scores may be a derived inter-marker heterogeneity metric.