Abstract: A method for providing a composite image of a single biological sample, comprising the steps of generating a first image of the biological sample with a target protein, generating a second image of the biological sample with a target nucleic acid sequence, and generating a composite image that provides the relative locations of both the target protein and the target nucleic acid sequence. Also provided is a method of analyzing a biological sample, comprising providing a composite image of the biological sample according to the method for providing a composite image, and analyzing the expression of the protein and the nucleic acid sequences of interest from the composite image. Further provided are systems and kits that comprise the means for executing the novel methods.

Abstract: The current disclosure provides methods for an automated clinical recommendation system that generates clinical recommendations for patients of a health care system based on natural language queries submitted by care providers of the health care system. The natural language queries may be typed into a user interface (UI) of the clinical recommendation system, or submitted by voice via a microphone. The clinical recommendation system provides a clinically explainable disease state of a patient based on patient data included in a query, and recommends a next course of action (e.g., a treatment) based on clinical guidelines and population statistics, in a manner that reduces a current burden of clinicians in consulting digital clinical manuals via a series of time-consuming and cumbersome interactions with a graphical user interface (GUI) of the digital clinical manuals.

Abstract: The present discussion relates to the design fabrication and use of synthetic scaffold structure for bone growth. In certain implementations the scaffold structures are comprised of a plurality of repeating structures each defined by a local topology. The local topologies are defined at a subset of points in their respective volumes by various parameters including, but not limited to, shape index, curvedness, mean curvature, and Gauss curvature.

Abstract: A method for determining a recurrence of a disease in a patient is presented. The method includes generating a plurality of medical images of an organ of the patient and determining a plurality of recurrence probabilities from the plurality of medical images. A recurrence of the disease is determined based on the plurality of recurrence probabilities and clinicopathological data of the patient using a Bayesian network.

Abstract: A method for determining a recurrence of a disease in a patient is presented. The method includes generating a plurality of medical images of an organ of the patient and determining a plurality of recurrence probabilities from the plurality of medical images. A recurrence of the disease is determined based on the plurality of recurrence probabilities and clinicopathological data of the patient using a Bayesian network.

Abstract: A method for determining a recurrence of a disease in a patient includes generating a medical image of an organ of the patient and then extracting an invasive edge around an area of interest in the medical image. A plurality of radiomics features is obtained from the invasive edge and the recurrence of the disease is determined based on the plurality of radiomics features.

Abstract: A method for generating an image of a region of interest in a biological sample comprising the steps of: generating a first image including the region of interest of the biological sample having undergone a first protocol but not a second protocol; and generating a second image including the region of interest of the biological sample after having undergone a second protocol; wherein the region of interest is smaller than said sample. Also provided is a method of analyzing a biological sample, comprising providing an image of the biological sample according to the method for generating an image of a region of interest in a biological sample, and analyzing the biological sample from the image. Further provided are system and kit that comprise the means for executing the novel methods.

Abstract: Various aspects and embodiments disclosed herein relate generally to the modelling, treatment, reducing resistance to the treatment, prevention, and diagnosis of diseases/symptoms related to ductal carcinoma in situ (DCIS). Embodiments include methods of detecting and/or treating diseases/symptoms related to ductal carcinoma in situ (DCIS), comprising the steps of: providing a sample of blood, cells, or tissue from a person suspected of having ductal carcinoma in situ; and detecting one or more epithelial markers in the sample.

Abstract: The subject matter of the present disclosure generally relates to techniques for image analysis. In certain embodiments, various morphological or intensity-based features as well as different thresholding approaches may be used to segment the subpopulation of interest and classify object in the images.

Abstract: The subject matter of the present disclosure generally relates to techniques for image analysis. In certain embodiments, various morphological or intensity-based features as well as different thresholding approaches may be used to segment the subpopulation of interest and classify object in the images.

Abstract: The present invention provides a microscope slide for analyzing a tissue sample. The slide includes an elongate planar substrate, which comprises a first major surface having a sample-affixing area within which a tissue sample may be affixed; a first positive control sample affixed on the first major surface at a first location adjacent to the sample-affixing area; and a second positive control sample affixed on the first major surface at a second location adjacent to the sample-affixing area. The first and second locations are spaced such that quality of the staining of the first and second positive control samples is indicative of the quality of the staining of the tissue sample. Also provided are a kit containing the microscope slide and a method of making and a method of using the microscope slide.

Abstract: Disclosed are novel computer-implemented methods for creating a blood vessel map of a biological tissue. The methods comprise the steps of, accessing image data corresponding to multi-channel multiplexed image of a fluorescently stained biological tissue manifesting expression levels of a primary marker and at least one auxiliary marker of blood vasculature, and extracting features of blood vessels using the primary marker as an input to create a single channel segmentation of the blood vessels. The method further comprises the steps of extracting features of blood vessels using the auxiliary marker to create auxiliary channels as a second input and apply multi-channel blood vessel enhancement. Blood vessel maps are created using the features and tracing the blood vasculature by iteratively extending the centerlines of the initial segmentation using statistical models and geometric rules.

Abstract: The disclosed embodiments are directed to a method for accurately counting and characterizing multiple cell phenotypes and sub-phenotypes within cell populations simultaneously by exploiting biomarker co-expression levels within cells of different phenotypes in the same tissue sample. The disclosed embodiments are also directed to a simple intuitive interface enabling medical staff (e.g., pathologists, biologists) to annotate and evaluate different cell phenotypes used in the algorithm and the presented through the interface.

Abstract: The present disclosure relates to characterization of biological samples. By way of example, a biological sample may be contacted with a plurality of probes specific for targets in the sample, such as probes for immune markers and segmenting probes. Acquired image data of the sample may be used to segment the images into epithelial and stromal regions to characterize individual cells in the sample based on the binding of the probes. Further, the biological sample may be characterized by a distribution, location, and type of a plurality of the characterized cells.

Abstract: Disclosed are novel computer-implemented methods for creating a blood vessel map of a biological tissue. The methods comprise the steps of, accessing image data corresponding to multi-channel multiplexed image of a fluorescently stained biological tissue manifesting expression levels of a primary marker and at least one auxiliary marker of blood vasculature, and extracting features of blood vessels using the primary marker as an input to create a single channel segmentation of the blood vessels. The method further comprises the steps of extracting features of blood vessels using the auxiliary marker to create auxiliary channels as a second input and apply multi-channel blood vessel enhancement.

Abstract: The disclosed embodiments are directed to a method for accurately counting and characterizing multiple cell phenotypes and sub-phenotypes within cell populations simultaneously by exploiting biomarker co-expression levels within cells of different phenotypes in the same tissue sample. The disclosed embodiments are also directed to a simple intuitive interface enabling medical staff (e.g., pathologists, biologists) to annotate and evaluate different cell phenotypes used in the algorithm and the presented through the interface.

Abstract: The present invention provides a microscope slide for analyzing a tissue sample. The slide includes an elongate planar substrate, which comprises a first major surface having a sample-affixing area within which a tissue sample may be affixed; a first positive control sample affixed on the first major surface at a first location adjacent to the sample-affixing area; and a second positive control sample affixed on the first major surface at a second location adjacent to the sample-affixing area. The first and second locations are spaced such that quality of the staining of the first and second positive control samples is indicative of the quality of the staining of the tissue sample. Also provided are a kit containing the microscope slide and a method of making and a method of using the microscope slide.

Abstract: A method of analyzing a biological sample suspected of having classic Hodgkin lymphoma, comprising (1) detecting, in a single sample, for the expression of at least two biomarkers selected from CD30, CD15, CD20, CD45, CD3, Pax-5, CD79A, BOB1 and OCT-2; and (b) analyzing the sample based on the presence, absence and/or expression level of the at least two biomarkers. Also provided is a method wherein all the nine biomarkers are analyzed on a single sample. Further provided are method for diagnosing classical Hodgkin lymphoma, as well as system and kit that comprise the means for executing the novel methods.

Abstract: The present disclosure relates to characterization of biological samples. By way of example, a biological sample may be contacted with a plurality of probes specific for targets in the sample, such as probes for immune markers and segmenting probes. Acquired image data of the sample may be used to segment the images into epithelial and stromal regions to characterize individual cells in the sample based on the binding of the probes. Further, the biological sample may be characterized by a distribution, location, and type of a plurality of the characterized cells.

Abstract: A method for providing a composite image of a single biological sample from a patient suspected of having classical Hodgkin lymphoma, comprising the steps of generating a first image of the biological sample including the presence, absence and/or expression level of a first biomarker, generating a second image of the biological sample including the presence, absence and/or expression level of a second biomarker, and generating a composite image that provides the relative location or expression of both biomarkers. Also provided is a method of analyzing a biological sample, comprising providing a composite image of the biological sample according to the method for providing a composite image, and analyzing the expression of the biomarkers of interest from the composite image. Further provided are method for diagnosing classical Hodgkin lymphoma, as well as system and kit that comprise the means for executing the novel methods.