Class / Patent application number | Description | Number of patent applications / Date published |
382129000 | DNA or RNA pattern reading | 28 |
20080253632 | Method of Detecting Precancerous Lesions - The present invention relates to methods of detection of precancerous lesions and/or cancer. The present invention also relates to the presence of DNA replication stress in precancerous lesions. The present invention further relates to the detection of loss of heterozygosity at common fragile sites and phosphorylated substrates of DNA damage activated kinases. | 10-16-2008 |
20080253633 | Aligning grids derived from fluorescent images of an array of signal sources - Disclosed are methods of processing images, and in particular aligning and orienting grids from a fluorescent array of signal sources, by linking nearest neighbor sources to form a hexagon, and then using the hexagon lines for alignment and orientation of the grid. Also disclosed are methods and algorithms for aligning image with grid and correcting for signal beads which are smaller than a grid field and the shift in a grid field. These methods can be used where the signal sources are fluorescent images from a microarray. Also disclosed are methods of automated watershed clustering following transformation. | 10-16-2008 |
20090110251 | COMPUTERIZED METHOD AND SYSTEM FOR ASSOCIATING A PORTION OF A DIAGNOSTIC IMAGE WITH AN ELECTRONIC RECORD - A computerized method for associating one or more portions of a diagnostic image with one or more electronic records is provided. The method includes receiving a diagnostic image having data particular to at least two persons and associating a first portion of the diagnostic image with an electronic record. The method may further include storing the first portion of the diagnostic image with the electronic record and/or associating and storing a common portion of the diagnostic image with the electronic record, the common portion consisting of data common to each person whose data is shown on the image. In one embodiment, the method may further include modifying the received diagnostic image and associating and storing the modified image with an electronic record. A computer system for associating at least a portion of a diagnostic image with an electronic record is also provided. | 04-30-2009 |
20090116714 | Animal cell colony picking apparatus and method - An apparatus and method for automated picking of animal cell colonies. A picking head comprising a plurality of hollow pins is provided. The apparatus has an integrated imager for capturing an image of adherent or non-adherent animal cell colonies held in liquid or semi-solid medium. Image processing identifies the locations of the animal cell colonies to be picked. Picking an animal cell colony is performed by aligning each of the hollow pins in turn with a target animal cell colony location, introducing the hollow pin into the medium, and aspirating the animal cell colony into the hollow pin. In the case of an adherent colony, the distal end of the pin is forced into oscillation to detach the animal cell colony prior to aspiration. The animal cell colony is dispensed into a well plate by increasing pressure in the fluid conduit. | 05-07-2009 |
20090129647 | METHODS AND SYSTEMS FOR IDENTIFICATION OF DNA PATTERNS THROUGH SPECTRAL ANALYSIS - Spectrogram extraction from DNA sequence has been known since 2001. A DNA spectrogram is generated by applying Fourier transform to convert a symbolic DNA sequence consisting of letters A, T, C, G into a visual representation that highlights periodicities of co-occurrence of DNA patterns. Given a DNA sequence or whole genomes, with this method it is easy to generate a large number of spectrogram images. However, the difficult part is to elucidate where are the repetitive patterns and to associate a biological and clinical meaning to them. The present disclosure provides systems and methods that facilitate the location and/or identification of repetitive DNA patterns, such as CpG islands, Alu repeats, tandem repeats and various types of satellite repeats. These repetitive elements can be found within a chromosome, within a genome or across genomes of various species. The disclosed systems and methods apply image processing operators to find prominent features in the vertical and horizontal direction of the DNA spectrograms. Systems and methods for fast, full scale analysis of the derived images using supervised machine learning methods are also disclosed. The disclosed systems and methods for detecting and/or classifying repetitive DNA patterns include: (a) comparative histogram method, (b) feature selection and classification using support vector machines and genetic algorithms, and (c) generation of spectrovideo from a plurality of spectral images. | 05-21-2009 |
20090175520 | METHOD AND APPARATUS FOR MATCHING OF BRACKETED PATTERNS IN TEST STRINGS - Disclose are a method of and system for matching input character sequences in a set of input patterns. The method comprises the steps of analyzing the set of input patterns, creating a pattern cluster look-up table (PCLT) based on said input patterns, and defining an offset value k. The PCLT is used to find, for each sequence s and offset k, a set of candidate patterns that can possibly match s, the set of candidate patterns is searched for patterns that match s, and all found matching patterns and sequences are reported. | 07-09-2009 |
20090175521 | Method and System for Creating and Embedding Information in Digital Representations of a Subject - Provided herein is a method for creating an adaptable digital representation of a subject, comprising: inputting into a computer system information sufficient to form a digital representation of the subject; deriving a digital representation of the subject based on the information; assigning traits to the digital representation; encoding the representation with the traits of the digital representation creating an encoded representation; and storing the encoded representation. | 07-09-2009 |
20100008554 | METHOD TO AUTOMATICALLY DECODE MICROARRAY IMAGES - A method of automatically identifying the microarray chip corners and probes, even if there are no probes at the corners, in a high density and high resolution microarray scanned image having an image space, wherein the method minimizes the error distortions in the image arising in the scanning process by applying to the image a multipass corner finding algorithm comprising: (a) applying a Radon transform to an input microarray image to project the image into an angle and distance space where it is possible to find the orientation of the straight lines; (b) applying a fast Fourier transform to the projected image of (a) to find the optimal tilting angle of the projected image; (c) determining the optimal first and last local maxima for the optimal tilting angle; (d) back projecting the determined first and last local maxima to the image space to find the first approximation of the first and last column lines of the image; (e) rotating the image and repeating steps (a) through (d) to find the first approximation of the top and bottom row lines of the image; (f) determining the first approximation of the four corners of the image from the intersection of the column and row lines; (g) applying a heuristic for determining if the first approximation of step (f) is sufficient; and (h) optionally trimming the scanned image around the first approximation of the four corners and repeating steps (a) through (f). | 01-14-2010 |
20100034444 | IMAGE ANALYSIS - Image processing for certain sequencing technologies requires data processing algorithms that provide fast sequence detection with low error rates. Methods and apparatus for performing image analysis for identifying nucleotide incorporations includes performing an image segmentation procedure on a plurality of data sets to identify sample objects and to create segmented data sets for each of the data sets. Each data set represents a sample image that includes a plurality of pixel locations and intensity data associated with each of the pixel locations. The segmented data sets represent identified sample objects for each one of the sample image data sets. An image registration procedure is performed on the segmented data sets to align the identified sample objects and to create data representative of the aligned identified sample objects. A strand formation procedure is then performed on the data representative of the aligned identified sample objects to identify nucleotide incorporations. | 02-11-2010 |
20100034445 | Continuous imaging of nucleic acids - The present invention relates to devices, systems, and methods for continuous imaging of nucleic acids. In one embodiment, the invention herein generally relates to a device for continuously imaging nucleic acids, the device including a rotating drum in which an exterior surface of the drum includes a plurality of color sensitive pixels. | 02-11-2010 |
20100074492 | METHODS AND APPARATUS FOR AUTOMATED BASE-CALLING ON MULTIPLE DNA STRANDS - In some aspects, a method of automated base-calling using at least one image obtained from a chemical sequencing process performed simultaneously on a plurality of DNA strands, the at least one image including intensity information corresponding to locations of at least one base in the plurality of DNA strands is provided. The method comprises processing the at least image to obtain a function corresponding to the intensity information in the at least one image for the at least one base, the function incorporating intensity information corresponding to each of the plurality of DNA strands, identifying a plurality of peaks in the function, the plurality of peaks indicating possible locations for the at least one base in the plurality of DNA strands, assigning membership to each of the plurality of peaks by determining whether each of the plurality of peaks is believed to have resulted from none, one or multiple of the plurality of DNA strands, and computing a sequence for the at least one base for each of the plurality of DNA strands based, at least in part, on the membership assignment. | 03-25-2010 |
20100266177 | SIGNAL PROCESSING BY ITERATIVE DECONVOLUTION OF TIME SERIES DATA - A signal processing method is provided and involves iteratively deconvoluting at least one digital signal data set with respect to time. A signal processor is also provided that can perform a signal processing method for iteratively deconvoluting at least one digital signal data set. Also provided is an instruction set readable by a machine, tangibly embodying a program of instructions executable by a machine to perform a signal processing method of iteratively deconvoluting at least one digital signal data set. Also provided is a data set readable by a machine, tangibly embodying a data set computed by a signal processing method for iteratively deconvoluting at least one digital signal data set. | 10-21-2010 |
20100296711 | METHOD OF DETERMINING A BIOSPECIES - Determining a biospecies is performed by using a plurality of analysis data obtained by analyzing a plurality of known samples whose corresponding biospecies are already revealed by a method of analyzing an organism and a determination threshold defined on the basis of the plurality of analysis data; deciding whether determination of a biospecies corresponding to an unknown sample is possible or not on the basis of the determination threshold; and determining a biospecies corresponding to the unknown sample on the basis of the plurality of analysis data when the determination is decided as possible. | 11-25-2010 |
20110235881 | Quantitative, multispectral image analysis of tissue specimens stained with quantum dots - A biological sample such as a tissue section is stained with one or more quantum dots and possibly other fluorophores (total number of fluorophores N). A camera coupled to a microscope generates an image of the specimen at a plurality of different wavelengths within the emission spectral band of the N fluorophores. An analysis module calculates coefficients C | 09-29-2011 |
20120020537 | DATA PROCESSING SYSTEM AND METHODS - Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies. | 01-26-2012 |
20130034284 | METHOD OF AND SYSTEM FOR ENHANCED DYNAMIC RANGE ASSAY ANALYSIS - The disclosed systems and methods allow composite images with enhanced dynamic range to be generated that result in more accurate, reliable, and efficient chemical and/or biological analyses. The disclosed systems include an image detector; a timer for tracking exposure time of the image detector; and computer readable medium, including instructions that when executed cause a computer system to generate a composite image using the multiple images of pixels. | 02-07-2013 |
20130142408 | Feature Intensity Reconstruction of Biological Probe Array - The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data. | 06-06-2013 |
20130202167 | METHOD AND APPARATUS FOR GENERATING GENE EXPRESSION PROFILE - A method and apparatus for generating a gene expression profile by obtaining data relating to phenotypes and data relating to gene expression from biological samples and statistically analyzing them together. | 08-08-2013 |
20140016843 | COMPUTER-ASSISTED KARYOTYPING - A system and method for computer-assisted karyotyping includes a processor which receives a digitized image of metaphase chromosomes for processing in an image processing module and a classifier module. The image processing module may include a segmenting function for extracting individual chromosome images, a bend correcting function for straightening images of chromosomes that are bent or curved and a feature selection function for distinguishing between chromosome bands. The classifier module, which may be one or more trained kernel-based learning machines, receives the processed image and generates a classification of the image as normal or abnormal. | 01-16-2014 |
20140072195 | AUTOMATED FISH READER USING LEARNING MACHINES - An automated reader for reading fluorescence in-situ hybridization signals includes one or more computer processors for receiving a digitized FISH image and executing the steps of converting colors within the image to a hue value, separately for each color extracting quantitative values to detect the presence of signals corresponding to spots and applying a plurality of algorithms to extract features from the signals to determine cell shapes and segment cells within the FISH image. After recombining the signals, the extracted features for the colors learning machines are used to classify the spots according to the color and separate merged signals of classified spots that are in close proximity to each other within the image. The classified spots are counted to determine relative frequency of colors and a report is generated providing the number of classified spots of each color. | 03-13-2014 |
20140153801 | METHOD AND COMPUTER PROGRAM PRODUCT FOR GENOTYPE CLASSIFICATION - A method for genotype classification including the steps of acquiring a pair of scanned images of an SNP sample for a plurality of individuals selected from a population, wherein one image of the image pairs is associated with a first allele and the other image of the image pair is associated with a second allele of the sample. For both images of the associated scanned image pair of each sample: performing pre-processing of the image to remove scanning noises from the image, obtaining total sample intensity information from the image, defining a sample boundary to encompass at least a substantial part of the luminous pixels of the image, matching said sample boundary to the image, and performing a pixel-based processing of the image using the matched sample boundary in order to obtain image quality information with respect to said sample. | 06-05-2014 |
20140233816 | METHODS AND SYSTEMS FOR BACKGROUND SUBTRACTION IN AN IMAGE - A method for improving image quality is provided. The method includes receiving image data of a substrate, wherein the image data is generated by imaging the substrate, and an image is generated from the image data. The method further includes generating a background representation from a background noise portion of the image, wherein the background portion includes signal information undesired for further processing and generating a background subtracted image by subtracting the background rep resentation from the image. In this way, a separate background image is not needed to subtract the background from the image including the regions-of-interest to improve image quality. | 08-21-2014 |
20140270435 | SPACIAL SEQUENCING/GENE EXPRESSION CAMERA - Methods, articles and systems that provide imagewise mapping or display of gene expression of a biosample, by contacting the biosample, such as a tissue slice or metacommunity, to a detector which captures material from the biosample and processes the captured material. In one embodiment the detector has an array of one or more capture sites at defined positions on the detector, each site carrying an immobilized capture oligonucleotide and a site-indexing oligonucleotide. The array captures mRNA from the biosample contacted thereto, and the captured mRNA is processed to form a sequenceable amount of amplified captured material which includes the site-indexing oligonucleotide, so that when sequenced, detection of the site-indexing oligonucleotide indicates the original capture location on the array, thereby mapping the sequenced material to its capture location and imaging display of gene expression distribution in the original biosample. In some embodiments the site-encoding sequence is integrated with the capture oligonucleotide. In other embodiments, the detector is a modified sequencing flow cell, which is opened to allow the biospecimen to be contacted to a capture surface; processing is performed while the material remains on the capture surface and locations of the resulting sequences correspond to the location of origin of the templates of the biomolecules in the sample. The spatially resolved sequencing, gene expression camera and technology in various embodiments are applied to genome sequences and DNA fragments present in the biosample, for example to study or diagnose developmental, disease, and tumor conditions. | 09-18-2014 |
20140369579 | ANALYSIS, SECURE ACCESS TO, AND TRANSMISSION OF ARRAY IMAGES - Systems and methods are provided the autocentering, autofocusing, acquiring, decoding, aligning, analyzing and exchanging among various parties, images, where the images are of arrays of signals associated with ligand-receptor interactions, and more particularly, ligand-receptor interactions where a multitude of receptors are associated with microparticles or microbeads. The beads are encoded to indicate the identity of the receptor attached, and therefore, an assay image and a decoding image are aligned to effect the decoding. The images or data extracted from such images can be exchanged between de-centralized assay locations and a centralized location where the data are analyzed to indicate assay results. Access to data can be restricted to authorized parties in possession of certain coding information, so as to preserve confidentiality. | 12-18-2014 |
20150063666 | Systems and Methods for Assessing Images - Disclosed are systems and methods for assessing images in applications such as microscopic scanning of a slide having light emitting objects. In certain embodiments, such scanning can involve objects such as sequencing beads disposed on the slide to facilitate biological analysis such as nucleic acid sequencing. Also disclosed are certain embodiments where images of light emitting objects are assessed for image quality so as to facilitate a feedback response such as a corrective action. In certain embodiments, such assessment and correction can be performed in real-time during the scanning process, and can include re-acquisition of the assessed image. Also disclosed are certain embodiments where such assessment and correction can be triggered dynamically during the scan, or before start of the scan, so as to enhance the scanning performance, including scanning time and throughput. | 03-05-2015 |
20150098637 | Feature Intensity Reconstruction of Biological Probe Array - The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data. | 04-09-2015 |
20150125053 | IMAGE ANALYSIS USEFUL FOR PATTERNED OBJECTS - A method of registering features in a repeating pattern can include (a) providing an object having a repeating pattern of features and a fiducial; (b) obtaining a target image of the object, wherein the target image includes the repeating pattern of features and the fiducial; (c) comparing the fiducial in the target image to reference data, wherein the reference data includes xy coordinates for a virtual fiducial; and (d) determining locations for the features in the target image based on the comparison of the virtual fiducial in the reference data to the fiducial in the data from the target image. The fiducial can have at least concentric circles that produce three different signal levels. The locations of the features can be determined at a variance of less than 5 μm. | 05-07-2015 |
20160055632 | METHODS AND SYSTEMS FOR DIGITALLY COUNTING FEATURES ON ARRAYS - Methods, systems and platforms for digital imaging of multiple regions of an array, and detection and counting of the labeled features thereon, are described. | 02-25-2016 |