Abstract: A diagnostic test system includes a housing, a reader, and a data analyzer. The housing includes a port constructed and arranged to receive a test strip that includes a flow path for a fluid sample, a sample receiving zone couple to the flow path, a label that specifically binds a target analyte, a detection zone coupled to the flow path and comprising a test region exposed for optical inspection and having an immobilized test reagent that specifically binds the target analyte, and at least one reference feature. The reader is operable to obtain light intensity measurements from exposed regions of the test strip when the test strip is loaded in the port.

Abstract: A method to calibrate measurements of a test analyte in a test sample including measuring at least one test-light level responsive to reactions of at least one reagent group and at least one reactive test analyte in the test sample and measuring at least one control-light level responsive to reactions of at least one reagent group and at least one control analyte in a control sample. Each control analyte is a known amount of at least one reactive test analyte. The method further includes determining a presence of the reactive test analyte in the test sample based on the measured test-light levels and control-light levels. The reagent group and the reactive test analyte react by attaching to each other.

Abstract: A method to calibrate measurements of a test analyte in a test sample including measuring at least one test-light level responsive to reactions of at least one reagent group and at least one reactive test analyte in the test sample and measuring at least one control-light level responsive to reactions of at least one reagent group and at least one control analyte in a control sample. Each control analyte is a known amount of at least one reactive test analyte. The method further includes determining a presence of the reactive test analyte in the test sample based on the measured test-light levels and control-light levels. The reagent group and the reactive test analyte react by attaching to each other.

Abstract: A diagnostic test system includes a housing, a reader, and a data analyzer. The housing includes a port constructed and arranged to receive a test strip that includes a flow path for a fluid sample, a sample receiving zone couple to the flow path, a label that specifically binds a target analyte, a detection zone coupled to the flow path and comprising a test region exposed for optical inspection and having an immobilized test reagent that specifically binds the target analyte, and at least one reference feature. The reader is operable to obtain light intensity measurements from exposed regions of the test strip when the test strip is loaded in the port.

Abstract: An assay test strip includes a flow path, a sample receiving zone, a label, a detection zone that includes a region of interest, and at least one position marker. The at least one position marker is aligned with respect to the region of interest such that location of the at least one position marker indicates a position of the region of interest. A diagnostic test system includes a reader that obtains light intensity measurement from exposed regions of the test strip, and a data analyzer that performs at least one of (a) identifying ones of the light intensity measurements obtained from the test region based on at least one measurement obtained from the at least one reference feature, and (b) generating a control signal modifying at least one operational parameter of the reader based on at least one measurement obtained from the at least one reference feature.

Abstract: A method to calibrate measurements of a test analyte in a test sample including measuring at least one test-light level responsive to reactions of at least one reagent group and at least one reactive test analyte in the test sample and measuring at least one control-light level responsive to reactions of at least one reagent group and at least one control analyte in a control sample. Each control analyte is a known amount of at least one reactive test analyte. The method further includes determining a presence of the reactive test analyte in the test sample based on the measured test-light levels and control-light levels. The reagent group and the reactive test analyte react by attaching to each other.

Abstract: A method to calibrate measurements of a test analyte in a test sample including measuring at least one test-light level responsive to reactions of at least one reagent group and at least one reactive test analyte in the test sample and measuring at least one control-light level responsive to reactions of at least one reagent group and at least one control analyte in a control sample. Each control analyte is a known amount of at least one reactive test analyte. The method further includes determining a presence of the reactive test analyte in the test sample based on the measured test-light levels and control-light levels. The reagent group and the reactive test analyte react by attaching to each other.

Abstract: An assay test strip includes a flow path, a sample receiving zone, a label, a detection zone that includes a region of interest, and at least one position marker. The at least one position marker is aligned with respect to the region of interest such that location of the at least one position marker indicates a position of the region of interest. A diagnostic test system includes a reader that obtains light intensity measurement from exposed regions of the test strip, and a data analyzer that performs at least one of (a) identifying ones of the light intensity measurements obtained from the test region based on at least one measurement obtained from the at least one reference feature, and (b) generating a control signal modifying at least one operational parameter of the reader based on at least one measurement obtained from the at least one reference feature.

Abstract: Provided herein, among other things, is method comprising: a) placing a planar absorbent support comprising an in vitro transcription and translation (IVTT) mix impregnated therein in contact with an array of in situ-assembled expression cassettes; and b) incubating the planar absorbent support and array under conditions by which the expressed cassettes are transcribed and translated by the impregnated IVTT components, thereby producing an array of proteins. Screening methods that employ the array of proteins are also provided.

Abstract: A method for determining the ploidy of a test genome is provided. In some embodiments, the method may comprises: a) obtaining a plurality of ratios for polymorphisms that are distributed throughout a test genome, wherein each of the ratios is a ratio of the measured copy number of uncut allele in a polymorphic site relative to the measured copy number of the uncut allele in the reference sample; b) taking the log of the ratios and plotting a distribution of the reference corrected log ratios of the SNP probes; and c) determining the ploidy of said the genome based on the number of peaks in that distribution.

Abstract: Provided herein is a set of reagents comprising: a plurality of at least three probe libraries, wherein each library of the plurality comprises one or more probe sets that are each specific for a target; and at least one of the libraries comprises a probe set that is present in another of the libraries. The plurality of libraries can be hybridized to spatially separated targets, simultaneously or sequentially. The identity of a spatially separated target can be determined by identifying which combination of the multiple libraries hybridize thereto.

Abstract: A method for determining the ploidy of a test genome is provided. In some embodiments, the method may comprises: a) obtaining a plurality of ratios for polymorphisms that are distributed throughout a test genome, wherein each of the ratios is a ratio of the measured copy number of uncut allele in a polymorphic site relative to the measured copy number of the uncut allele in the reference sample; b) taking the log of the ratios and plotting a distribution of the reference corrected log ratios of the SNP probes; and c) determining the ploidy of said the genome based on the number of peaks in that distribution.

Abstract: A test system includes an optical medium, a binding agent capable of capturing a target complex, and a light detector. The optical medium provides a light path, and the binding agent is positioned to hold the target complex in an evanescent field created by propagation of light along the light path. The complex interacts with the evanescent field and emits light that the detector positioned to detect. The optical medium and the detector can be included in an optical integrated circuit where detected light passes through the optical medium transverse to the direction of the light path.

Abstract: A method for positioning a tip of an atomic force microscope relative to a intracellular target site in a cell is provided. In general terms, the method comprises: a) positioning a fluorescent tip of an atomic force microscope over a cell comprising a fluorescent intracellular target site so that said tip is above target site; b) moving the tip toward said target site while obtaining images of the distal end of said tip and/or the target site using a fluorescence microscope; and c) arresting the movement of the tip when the target site and the distal end of the tip are both in focus in the fluorescence microscope. A microscope system for performing the method is also provided.

Abstract: A method for positioning a tip of an atomic force microscope relative to a intracellular target site in a cell is provided. In general terms, the method comprises: a) positioning a fluorescent tip of an atomic force microscope over a cell comprising a fluorescent intracellular target site so that said tip is above target site; b) moving the tip toward said target site while obtaining images of the distal end of said tip and/or the target site using a fluorescence microscope; and c) arresting the movement of the tip when the target site and the distal end of the tip are both in focus in the fluorescence microscope. A microscope system for performing the method is also provided.

Abstract: Methods, systems, and computer readable media for determining the quality of a CGH array, including calculating a spread of the derivative of log ratio value differences between consecutive probes representing consecutive positions along a chromosome, wherein ratio values are calculated from probe signals from a CGH array.

Abstract: A method of estimating the allele-specific copy number of a SNP in a test genome is provided. In certain embodiments, the method involves: a) calculating a plurality of probability distribution functions that fit a plurality of log ratios indicating which alleles of a plurality of single nucleotide polymorphisms (SNPs) are present in diploid regions of a test and reference genome; and b) estimating the allele-specific copy number of a SNP of the test genome using said plurality of probability distribution functions.

Abstract: An assay test strip includes a flow path, a sample receiving zone, a label, a detection zone that includes a region of interest, and at least one position marker. The at least one position marker is aligned with respect to the region of interest such that location of the at least one position marker indicates a position of the region of interest. A diagnostic test system includes a reader that obtains light intensity measurement from exposed regions of the test strip, and a data analyzer that performs at least one of (a) identifying ones of the light intensity measurements obtained from the test region based on at least one measurement obtained from the at least one reference feature, and (b) generating a control signal modifying at least one operational parameter of the reader based on at least one measurement obtained from the at least one reference feature.

Abstract: Aspects of the disclosure are generally directed to methods, probes, probe compositions and kits for detecting or quantifying target oligonucleotides. In some embodiments, there are provided methods for determining the level of target oligonucleotides, such as a small RNA (e.g., miRNA), in a sample. In some embodiments, the methods comprise analyzing hybridization of target oligonucleotides to a test microarray; analyzing hybridization of a known amount of reference oligonucleotides (having the same sequences as the target oligonucleotides) to a calibration microarray; and determining the level of the target oligonucleotides in the sample by comparing the hybridization of the target oligonucleotides with the hybridization of the reference oligonucleotides.

Abstract: An assay test strip includes a flow path, a sample receiving zone, a label, a detection zone that includes a region of interest, and at least one position marker. The at least one position marker is aligned with respect to the region of interest such that location of the at least one position marker indicates a position of the region of interest. A diagnostic test system includes a reader that obtains light intensity measurement from exposed regions of the test strip, and a data analyzer that performs at least one of (a) identifying ones of the light intensity measurements obtained from the test region based on at least one measurement obtained from the at least one reference feature, and (b) generating a control signal modifying at least one operational parameter of the reader based on at least one measurement obtained from the at least one reference feature.