Abstract: Identification of regions-of-interest within cell maps is disclosed. In certain embodiments, identification of the regions-of interest is based on the use of biomarkers selected based on nucleic acid sequence data. The nucleic acid sequence data may be acquired for a homogeneous or heterogeneous set of cells present in the respective tissue sample.

Abstract: The invention generally relates to methods and kits for capturing sperm nucleic acids from or in a biological sample. In one embodiment the method the method comprises, contacting the sample with a lysis solution, having a protamine-DNA complex, to lyse the cell and applying a protamine-specific binding element. This results in the protamine-specific binding element binding to the protamine-DNA to form a complex which may be captured, purified, or detected. Also provided are kits for carrying out the disclosed methods.

Abstract: The invention generally relates to methods and kits for capturing sperm nucleic acids from or in a biological sample. In one embodiment the method the method includes, contacting the sample with a lysis solution, having a protamine-DNA complex, to lyse the cell and applying a protamine-specific antibody. This results in the protamine-specific antibody binding to the protamine-DNA to form a complex which may be captured, purified, or detected. Also provided are kits for carrying out the disclosed methods.

Abstract: A method of capturing a sperm deoxyribo nucleic acid (DNA) in a sample is disclosed. The method includes a step of contacting a lysis solution to the sample that includes at least a sperm cell or a sperm cell lysate to lyse the sperm cell. The sperm cell or sperm cell lysate includes a protamine-DNA complex. The method further includes applying at least a protamine-specific antibody to the lysed sperm cell, wherein the protamine-specific antibody binds to the protamine-DNA complex of the lysed sperm cell to form an antibody-protamine-DNA complex. The method further includes capturing the antibody-protamine-DNA complex; and isolating and detecting the sperm DNA from the captured antibody-protamine-DNA complex.

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: Methods for detecting a plurality of targets in a biological sample are provided. The method comprises contacting the biological sample with a plurality of target-binding probes to form a plurality of target-bound probes, covalently attaching at least one of the target-bound probes to the biological sample, and observing the signals from the target-bound probes sequentially. An associated kit and device for detection of the plurality of targets are also provided.

Abstract: Identification of regions-of-interest within cell maps is disclosed. In certain embodiments, identification of the regions-of interest is based on the use of biomarkers selected based on nucleic acid sequence data. The nucleic acid sequence data may be acquired for a homogeneous or heterogeneous set of cells present in the respective tissue sample.

Abstract: The invention generally relates to methods and kits for capturing sperm nucleic acids from or in a biological sample. In one embodiment the method the method comprises, contacting the sample with a lysis solution, having a protamine-DNA complex, to lyse the cell and applying a protamine-specific antibody. This results in the protamine-specific antibody binding to the protamine-DNA to form a complex which may be captured, purified, or detected. Also provided are kits for carrying out the disclosed methods.

Abstract: A method is provided herein, wherein the method of capturing a sperm deoxyribo nucleic acid (DNA) in a sample, comprises contacting a lysis solution to the sample comprising at least a sperm cell or a sperm cell lysate to lyse the sperm cell. The sperm cell or sperm cell lysate comprises a protamine-DNA complex. The method further comprises applying at least a protamine-specific antibody to the lysed sperm cell, wherein the protamine-specific antibody binds to the protamine-DNA complex of the lysed sperm cell to form an antibody-protamine-DNA complex. The antibody binding is followed by capturing the antibody-protamine-DNA complex; and isolating and detecting the sperm DNA from the captured antibody-protamine-DNA complex.

Abstract: Disclosed are high throughput methods of probing multiple targets in a biological sample where the recurrent time-consuming antibody incubation steps and individual signal modification and activation steps are replaced by simultaneous hybridization of biomarkers and sequential detection by combining signal removal and activation into a single step. Also disclosed are images obtained by such methods.

Abstract: Methods for detecting a plurality of targets in a biological sample are provided. The method comprises contacting the biological sample with a plurality of target-binding probes simultaneously to form a plurality of target-bound probes and observing the signals from the target-bound probes sequentially. An associated kit and device for detection of the plurality of targets are also provided.

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 high throughput methods of probing multiple targets in a biological sample where the recurrent time-consuming antibody incubation steps and individual signal modification and activation steps are replaced by simultaneous hybridization of biomarkers and sequential detection by combining signal removal and activation into a single step. Also disclosed are images obtained by such methods.

Abstract: The present techniques include methods and systems for finding correspondences between tissue spots in tissue microarray serial sections belonging to the same recipient block. The present techniques may also be used to relate individual tissue cores to clinical information. Using either a whole slide image or the relative x-y coordinates of the tissue spots on the slide, individual tissue spots in different tissue microarrays may be linked to one another and their clinical information.

Abstract: Methods for detecting multiple targets in a biological sample are provided. The methods includes contacting the sample with a first probe; physically binding the first probe to a first target; observing a first signal from the first probe; applying a chemical agent to modify the first signal; contacting the sample with a second probe; physically binding the second probe to a second target; and observing a second signal from the second probe. The methods disclosed herein also provide for multiple iterations of binding, observing, signal modification for deriving information about multiple targets in a single sample. An associated kit and device are also provided.

Abstract: Novel methods of probing multiple targets in a biological sample are provide whereby the targets are DNA, RNA and protein. The method comprises subjecting the sample to an in situ hybridization reaction using a labeled nucleic acid probe that binds an RNA target, observing a signal, and optionally removing the signal. The method further comprises an antigen retrieval protocol, observing a signal, removing the signal, and optionally applying a protease treatment to access the sample's DNA targets by subjecting the sample to an in situ hybridization reaction using a labeled nucleic acid probe, observing a signal from the labeled DNA targets, and optionally removing the signal.

Abstract: The compositions described include an antibody diluent buffer that minimizes the amount of antibody required for immunoassays and further improves the performance of antibody-based assays. The claimed antibody diluent buffer comprises a high-molecular weight neutral polymer and an antibody that specifically binds to an antigen of interest, wherein the antibody remains in solution in the presence of the polymer. Methods for the use of the antibody diluent buffer to detect an antigen, even trace amounts of an antigen, in an antibody-based assay are also disclosed herein.

Abstract: The present techniques provide systems and methods for registering images of tissue spots on a tissue microarray (TMA). In studies involving multiple biomarkers being studied on the same TMA, the TMA slide is removed from the microscope, stained, and then imaged, often multiple times. The present techniques relate to validation of the registration of the acquired images of the same TMA. An automatic approach to register the images and detect registration failures as provided herein may enhance the rapid analysis of the tissues. Artifacts such as tissue folding and tissue loss are also determined automatically.

Abstract: The invention relates generally to a process of analyzing and visualizing the expression of biomarkers in individual cells wherein the cells are examined to develop patterns of expression by using a grouping algorithm, and a system to perform and display the analysis.

Abstract: A method for generating a brightfield type image, which resembles a brightfield staining protocol of a biological sample, using fluorescent images is provided. The steps comprise acquiring two or more fluorescent images of a fixed area on a biological sample, mapping said fluorescent image into a brightfield color space, and generating a bright field image. Also provided is an image analysis system for generating a brightfield type image of a biological sample using fluorescent images.