Abstract: Provided herein are methods of activating immune cells. The method includes providing a population of immune cells and contacting the population of immune cells with a first agent and a second agent. The first agent includes an immune cell activator attached to a first binder moiety, and the second agent includes at least one capture oligomer. The at least one capture oligomer is capable of associating with the first binder moiety. Also provided are kits for activating immune cells.

Abstract: The invention discloses a method for reduction of autofluorescence in biological samples, comprising the steps of: a) providing a biological microscopy sample; b) irradiating the sample with visible light, wherein the visible light has a spectrum such that at least 50% of the light intensity emanates from a narrow wavelength interval within the visible range. The invention also discloses a method for autofluorescence reduction with triplet sensitizers irradiated with visible light.

Abstract: The present invention relates to a microbubble complex comprising a microbubble having an outer shell comprising a mixture of native and denatured albumin encapsulating a perfluorocarbon gas, a therapeutic agent, a bifunctional linker having one end attached to the therapeutic agent and the other attached to a ligand and wherein the ligand is bound to the other shell of the microbubble through hydrophobic interactions. Also included are methods for delivering the aforementioned microbubble complex to a tissue target.

Abstract: Provided herein are methods of activating immune cells. The method includes providing a population of immune cells and contacting the population of immune cells with a first agent and a second agent. The first agent includes an immune cell activator attached to a first binder moiety, and the second agent includes at least one capture oligomer. The at least one capture oligomer is capable of associating with the first binder moiety. Also provided are kits for activating immune cells.

Abstract: Methods comprising the use of photoactivated chemical bleaching for detecting multiple targets in a biological sample are provided. The methods include the steps of binding at least one probe to one or more target present in a biological sample including multiple targets, and detecting a signal from the probe. The method further includes the steps of contacting the sample comprising the bound probe with a photoinitiator and irradiating the sample, thereby initiating a photoactivated chemical bleaching process that substantially inactivates the probe. The method further includes the steps of binding at least one probe to one or more target present in the sample, and detecting a signal from the probe. The process of binding, detecting and bleaching may be iteratively repeated.

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: Provided are methods and kits for activating T cells, the method comprising providing a population of T cells, adding a plurality of first agents, where the first agent comprises a T-cell activator and a first binder moiety, and adding a second agent comprising a plurality of capture oligomers, where at least a segment of at least one of the plurality of capture oligomers is capable of associating with the first binder moiety. The method further comprises incubating the population of T cells, whereby at least a portion of the population of T cells is activated.

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 relates to a microbubble complex comprising a microbubble having an outer shell comprising a mixture of native and denatured albumin encapsulating a perfluorocarbon gas, a therapeutic agent, a bifunctional linker having one end attached to the therapeutic agent and the other attached to a ligand and wherein the ligand is bound to the other shell of the microbubble through hydrophobic interactions. Also included are methods for delivering the aforementioned microbubble complex to a tissue target.

Abstract: Methods comprising the use of photoactivated chemical bleaching for detecting multiple targets in a biological sample are provided. The methods include the steps of providing a biological sample including multiple targets, binding at least one probe to one or more target present in the sample, and detecting a signal from the probe. The method further includes the steps of contacting the sample comprising the bound probe with an electron transfer reagent, as well as an optional additive which prevents target modification during photoactivated chemical bleaching, and irradiating the sample, thereby initiating a photoreaction that substantially inactivates the probe by photoactivated chemical bleaching. The method further includes the steps of binding at least one probe to one or more target present in the sample, and detecting a signal from the probe. The process of binding, defecting and bleaching may be iteratively repeated.

Abstract: Methods comprising the use of photoactivated chemical bleaching for detecting multiple targets in a biological sample are provided. The methods include the steps of providing a biological sample containing multiple targets, binding at least one probe to one or more target present in the sample, and observing a signal from the probe. The method further includes the steps of contacting the sample comprising the bound probe with a cationic or zwitterionic borate compound and irradiating the sample, thereby initiating a photoreaction that substantially inactivates the probe by photoactivated chemical bleaching. The method further includes the steps of binding at least one probe to one or more target present in the sample, and observing a signal from the probe. The process of binding, observing and bleaching may be iteratively repeated.

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 present invention relates to a microbubble complex comprising a microbubble having an outer shell comprising a mixture of native and denatured albumin encapsulating a perfluorocarbon gas, a therapeutic agent, a bifunctional linker having one end attached to the therapeutic agent and the other attached to a ligand and wherein the ligand is bound to the other shell of the microbubble through hydrophobic interactions. Also included are methods for delivering the aforementioned microbubble complex to a tissue target.

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: Methods comprising probing multiple targets in an H&E stained biological sample are provided. The methods include the steps of providing a hematoxylin and eosin stained biological sample containing multiple targets, optionally detecting H&E staining of the sample, removing the hematoxylin and eosin signals, and detecting additional features or targets in the biological sample. The detecting step may include performing the steps of binding at least one probe to one or more targets to the sample, detecting a signal from the probe and contacting the sample with a bleaching agent. The process of binding, detecting and bleaching may be iteratively repeated.

Abstract: Provided are methods and kits for activating T cells, the method comprising providing a population of T cells, adding a plurality of first agents, where the first agent comprises a T-cell activator and a first binder moiety, and adding a second agent comprising a plurality of capture oligomers, where at least a segment of at least one of the plurality of capture oligomers is capable of associating with the first binder moiety. The method further comprises incubating the population of T cells, whereby at least a portion of the population of T cells is activated.

Abstract: A borate compound for use as photoinduced chemical bleaching reagent is disclosed having improved bleaching performance under certain conditions, compared to neutral borates. The compounds are comprised of Formula I; R1R2R3R4BXa?? I where each R1, R2, and R3 and R4 is, independently, an alkyl, alkylaryl, or arylalkyl, with the proviso that at least one of R1, R2, and R3 and R4 is an alkyl group and at least two of R1, R2, R3 and R4 group is positively charged; X is an anion; and a equals 1, 2, or 3.

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: The invention discloses a method for reduction of autofluorescence in biological samples, comprising the steps of: a) providing a biological microscopy sample; b) irradiating the sample with visible light, wherein the visible light has a spectrum such that at least 50% of the light intensity emanates from a narrow wavelength interval within the visible range. The invention also discloses a method for autofluorescence reduction with triplet sensitizers irradiated with visible light.

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.