Abstract: Methods of assessing the suitability of a fluorochrome panel for use in a flow cytometric protocol analyzing a biological sample are provided. Methods of interest include, with a processor, receiving an initial fluorochrome panel, a plurality of population identifiers each referring to a particle population, and an instrument identifier. Methods additionally include, creating a set of population-marker pairs, generating a set of separability metrics each predicting a measure of statistical distance between particle populations in flow cytometer data space, aggregating the set of separability metrics into a panel score, and evaluating the panel score. Systems and non-transitory computer readable storage media for assessing the suitability of a fluorochrome panel for use in a flow cytometric protocol analyzing a biological sample are also provided.

Abstract: The present disclosure provides a support shelf for a histological container for use with multiple histological samples. The container can include shelf supports on interior sides of the container and orient the shelf at a downward angle for fluid flow. The shelf can support a plurality of sample slides across a support surface. The shelf can include an end support to maintain the slide on the support surface. To control fluid flow across the slide, the end support can encourage wicking to a wicking end support of the shelf in a controlled manner to maximize exposure of the specimen to the reagent and other fluids and reduce costs and expense of processing. Side rails at the side of the shelf help maintain slides on the shelf, and guide rails disposed inwardly from the side rails help maintain separation of the multiple slides placed on the shelf support surface.

Abstract: A histological container for histological samples is provided with a removable humidity control lid with portals for access into the container. The lid creates a humidified zone across the lid portals to allow processing steps inside the container while minimizing variations in the container humidity. A cover can be placed over the container for thermal control inside the container. The cover includes a top with portals aligned with the lid portals for access through the cover and top to inside the container. The cover can include a shutter slidably interfaced with the top. The shutter can include shutter portals selectively aligned with the top portals. Slidable alignment of the shutter portals with the top portals allows access to inside the container. Slidable nonalignment of the shutter portals with the top portals restricts access, essentially closing the container to control temperature levels and other ambient conditions inside the container.

Abstract: The present disclosure provides a cover pad for a histological container having an inclined shelf for a planar support with a histological sample coupled to a topside of the planar support and a cover pad over the planar support. The cover pad is generally planar with flow guiding surfaces that intersect downward flowing fluids deposited on the planar support. A spreader surface on the cover pad disperses fluids toward the cover pad sides. The spreader surface can be angled upward, as a convex curve, to direct impinging fluids along the angled surface toward the sides. Side flow guides intersect the spreader surface angle and smoothly flow the sideways directed fluids into a vertical space between the cover pad and the planar support. Side flow bars extend longitudinally upward above the side flow guides and assist in retaining fluids onto the planar support before the fluids engage the side flow guides.

Abstract: A support tile for a container for use with histological samples can be held at a downwardly inclined angle. A planar support, having a histological sample coupled to an underside, can be supported by the support tile with a space therebetween for fluids to flow through. The support tile top includes an inclined ramp for fluid deposition, beginning a flow path down the support tile. A spreader step disperses fluids more uniformly across the support tile. The spreader step can be angled, such as convex, facing the flow path direction and delay the fluid flow through the flow path central portion until flow is dispersed to the flow path sides for more uniform flow across the sample. An aggregator at a support tile bottom directs fluid flow from sides toward the flow path central portion for wicking of the fluid by an end stop to drain from the support tile.

Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.

Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) labelling the planar sample with a capture agent that is linked to a nucleic acid, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the nucleic acid, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.

Abstract: Disclosed herein include systems, devices, and methods for determining a gating strategy. An acquisition system can cause a particle analyzer to collect parameter measurements of some particles of a sample. An analysis system can receive the parameter measurements and determine a gating strategy from the parameter measurements. The acquisition can collect measurements of some or all of the remaining particles of the sample using the gating strategy determined by the analysis system.

Abstract: Disclosed herein include systems, devices, and methods for determining a gating strategy. An acquisition system can cause a particle analyzer to collect parameter measurements of some particles of a sample. An analysis system can receive the parameter measurements and determine a gating strategy from the parameter measurements. The acquisition can collect measurements of some or all of the remaining particles of the sample using the gating strategy determined by the analysis system.

Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) labelling the planar sample with a capture agent that is linked to a nucleic acid, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the nucleic acid, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.

Abstract: Disclosed herein include systems, devices, and methods for determining a gating strategy. An acquisition system can cause a particle analyzer to collect parameter measurements of some particles of a sample. An analysis system can receive the parameter measurements and determine a gating strategy from the parameter measurements. The acquisition can collect measurements of some or all of the remaining particles of the sample using the gating strategy determined by the analysis system.

Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.

Abstract: Disclosed herein include systems, devices, and methods for determining a gating strategy. An acquisition system can cause a particle analyzer to collect parameter measurements of some particles of a sample. An analysis system can receive the parameter measurements and determine a gating strategy from the parameter measurements. The acquisition can collect measurements of some or all of the remaining particles of the sample using the gating strategy determined by the analysis system.

Abstract: Provided herein is a method and system for analyzing a sample. In some embodiments the method makes use of a plurality of capture agents that are each linked to a different oligonucleotide and a corresponding plurality of labeled nucleic acid probes, wherein each of the labeled nucleic acid probes specifically hybridizes with only one of the oligonucleotides. The sample is labeled with the capture agents en masse, and sub-sets of the capture agents are detected using iterative cycles using corresponding subsets of the labeled nucleic acid probes.

Abstract: Aspects of the present disclosure include methods for processing and scaling cytometric data. Methods according to certain embodiments include obtaining cytometric data for a sample, wherein the cytometric data comprises measurements of a plurality of parameters from particles irradiated in the sample flowing in a flow stream; identifying a parameter of interest; specifying positive and negative measurement intervals on the parameter of interest; scaling the cytometric data by transforming the parameter of interest based at least in part on the corresponding specified positive and negative intervals. Systems for practicing the subject methods are also provided. Non-transitory computer readable storage mediums are also described.

Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.

Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) labelling the planar sample with a capture agent that is linked to a nucleic acid, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the nucleic acid, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.

Abstract: The tissue microenvironment is a critical factor to disease mechanism and therapeutic efficiency. Provided here is an imaging platform, methods, and kits which enable measurement of tens of parameters simultaneously within a single tissue, with the potential to reveal unique and important biological associations related to the spatial dimension. The sensitivity of the platform, methods, and kits described herein extends to measure low level markers which can be important for tracking disease progression, diagnosing disease, or both.