Abstract: A computer-based specimen analyzer (10) is configured to detect a level of expression of genes in a cell sample by detecting dots that represent differently stained genes and chromosomes in a cell. The color of the stained genes and the chromosomes is enhanced and filtered to produce a dot mask that defines areas in the image that are genes, chromosomes, or non-genetic material. Metrics are determined for the dots and/or pixels in the image of the cell in areas corresponding to the dots. The metrics are fed to a classifier that separates genes from chromosomes. The results of the classifier are counted to estimate the expression level of genes in the tissue samples.

Abstract: A computer-based specimen analyzer (10) is configured to detect a level of expression of genes in a cell sample by detecting dots that represent differently stained genes and chromosomes in a cell. The color of the stained genes and the chromosomes is enhanced and filtered to produce a dot mask that defines areas in the image that are genes, chromosomes, or non-genetic material. Metrics are determined for the dots and/or pixels in the image of the cell in areas corresponding to the dots. The metrics are fed to a classifier that separates genes from chromosomes. The results of the classifier are counted to estimate the expression level of genes in the tissue samples.

Abstract: Processing of images acquired via fluorescence microscopy by identifying broadband and other undesired signals from the component signals of a scanned image, and processing selected regions of the image that are known to contain signals of interest, thereby extracting or identifying desired signals while subtracting undesired signals. One or more broadband signals are recognized by their unique signature and ubiquitous dispersion through the image. Regions of the scanned image may be tagged as consisting of predominantly broadband signals and are ignored during a spectral unmixing process. The remaining regions of the image, or selected regions of the image known to contain desired signals, may be unmixed, and the plurality of reference spectra subtracted from the components to extract or identify the target signals. The set of target signals may be refined by eliminating known or obvious sources of noise by, for instance, being compared to known or ideal sets of signals from similar materials.

Abstract: Embodiments of a system, method, and kit for visualizing a nucleus are disclosed. A tissue sample is pretreated with a protease to permeabilize the nucleus, and then incubated with a nanoparticle/DNA-binding moiety conjugate. The DNA-binding moiety includes at least one DNA-binding molecule. The conjugate binds to DNA within the nucleus, and the nanoparticle is visualized, thereby visualizing the nucleus. Computer and image analysis techniques are used to evaluate nuclear features such as chromosomal distribution, ploidy, shape, size, texture features, and/or contextual features. The method may be used in combination with other multiplexed tests on the tissue sample, including fluorescence in situ hybridization. Kits for performing the method include a protease enzyme composition, a nanoparticle/DNA-binding moiety conjugate, and a reaction buffer.

Abstract: A method and system for spectral demultiplexing of fluorescent species, such as quantum dots, conjugated with a biological tissue. The process of demultiplexing involves a non-liner regression based on curve-fitting of estimated spectra of the quantum dots and confidence intervals describing the parameters of such fitting curve for typical quantum dots.

Abstract: An imaging system (100) is capable of detecting of tissue situated on a microscope slide (180). The imaging system (100) includes a light source (150), an image capturing device (160) including a camera, and an imaging lens (170). The light source (150) directs light (154) towards one or more of the edges of the slide (180) such that the light (154) undergoes total internal reflection between a surface of the slide (180) and a coverslip (182) carried by the slide (180). The light (154) has a wavelength or waveband designed to stimulate one or more specimens carried on the slide (180). The imaging lens (170) is positioned to direct radiation emitted from the tissue and/or fluorophore onto the camera. The image capturing device (160) can capture an image of the whole slide (180) or a portion thereof.

Abstract: Processing of images acquired via fluorescence microscopy by identifying broadband and other undesired signals from the component signals of a scanned image, and processing selected regions of the image that are known to contain signals of interest, thereby extracting or identifying desired signals while subtracting undesired signals. One or more broadband signals are recognized by their unique signature and ubiquitous dispersion through the image. Regions of the scanned image may be tagged as consisting of predominantly broadband signals and are ignored during a spectral unmixing process. The remaining regions of the image, or selected regions of the image known to contain desired signals, may be unmixed, and the plurality of reference spectra subtracted from the components to extract or identify the target signals. The set of target signals may be refined by eliminating known or obvious sources of noise by, for instance, being compared to known or ideal sets of signals from similar materials.

Abstract: Embodiments of a system, method, and kit for visualizing a nucleus are disclosed. A tissue sample is pretreated with a protease to permeabilize the nucleus, and then incubated with a nanoparticle/DNA-binding moiety conjugate. The DNA-binding moiety includes at least one DNA-binding molecule. The conjugate binds to DNA within the nucleus, and the nanoparticle is visualized, thereby visualizing the nucleus. Computer and image analysis techniques are used to evaluate nuclear features such as chromosomal distribution, ploidy, shape, size, texture features, and/or contextual features. The method may be used in combination with other multiplexed tests on the tissue sample, including fluorescence in situ hybridization. Kits for performing the method include a protease enzyme composition, a nanoparticle/DNA-binding moiety conjugate, and a reaction buffer.

Abstract: A computer-based specimen analyzer (10) is configured to detect a level of expression of genes in a cell sample by detecting dots that represent differently stained genes and chromosomes in a cell. The color of the stained genes and the chromosomes is enhanced and filtered to produce a dot mask that defines areas in the image that are genes, chromosomes, or non-genetic material. Metrics are determined for the dots and/or pixels in the image of the cell in areas corresponding to the dots. The metrics are fed to a classifier that separates genes from chromosomes. The results of the classifier are counted to estimate the expression level of genes in the tissue samples.

Abstract: A method and system for spectral demultiplexing of fluorescent species, such as quantum dots, conjugated with a biological tissue. The process of demultiplexing involves a non-liner regression based on curve-fitting of estimated spectra of the quantum dots and confidence intervals describing the parameters of such fitting curve for typical quantum dots.

Abstract: Embodiments of a system, method, and kit for visualizing a nucleus are disclosed. A tissue sample is pretreated with a protease to permeabilize the nucleus, and then incubated with a nanoparticle/DNA-binding moiety conjugate. The DNA-binding moiety includes at least one DNA-binding molecule. The conjugate binds to DNA within the nucleus, and the nanoparticle is visualized, thereby visualizing the nucleus. Computer and image analysis techniques are used to evaluate nuclear features such as chromosomal distribution, ploidy, shape, size, texture features, and/or contextual features. The method may be used in combination with other multiplexed tests on the tissue sample, including fluorescence in situ hybridization. Kits for performing the method include a protease enzyme composition, a nanoparticle/DNA-binding moiety conjugate, and a reaction buffer.

Abstract: A digital image collection system and method includes an area scan camera that scans a region to obtain digital image data therefrom, the area scan camera having an optical scan axis. A specimen mounting unit receives a specimen that is mounted on a top surface thereof, for enabling the specimen to be scanned by the area scan camera. The top surface of the specimen mounting unit is slanted at an angle with respect to the area scan camera such that the optical scan axis is oblique to the top surface of the specimen mounting unit.

Abstract: A method of segmenting objects in an image is described. The method applies a Top Hat algorithm to the image then constructs inner and outer markers for application to the original image in a Watershed algorithm. The inner marker is constructed using binary erosion. The outer marker is constructed using binary dilation and perimeterisation. The method finds particular application for first level segmentation of a cell nucleus prior to detailed analysis.

Abstract: A method of segmentation of cell nuclei is described that uses an active contours approach based on a Viterbi search algorithm. Also disclosed is an initialisation technique that maximises the probability of a correct segmentation. The invention also includes a method to classify cell nuclei according to the difficulty of correct segmentation. Nuclei that are difficult to segment can be rejected to minimise the probability of false positives. The probability of false positives can be driven close to 0%.

Abstract: A method of segmenting objects in an image is described. The method applies a Top Hat algorithm to the image then constructs inner and outer markers for application to the original image in a Watershed algorithm. The inner marker is constructed using binary erosion. The outer marker is constructed using binary dilation and perimeterisation. The method finds particular application for first level segmentation of a cell nucleus prior to detailed analysis.