Abstract: 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.

Abstract: A method to be implemented on or in a computer is disclosed, where the method includes data collection, calibration, candidate selection, and analysis of data streams associated with each candidate to classify single molecule fluorescence resonance energy transfer events. Once classified, the classification can be related to the nature of the events, such as the identification of dNTP incorporation during primer extension to obtain a base read out of an unknown template.

Abstract: 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.

Abstract: 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.

Abstract: An automated laboratory slide management and interpretation system and method in which slides are stained and then digitally imaged and the images are interpreted prior to referral to a diagnostician or placement in storage. The interpretation of the images involves the application of pattern recognition principles to compare the digitized images to known sample patterns from a variety of sources. Additionally, based on the results of the interpretation, the slide may undergo additional testing or staining, and additional samples may be prepared and tested. The specimens may be delivered to the diagnostician along with a tentative diagnosis.

Abstract: 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 approximati

Abstract: A particle image analyzing apparatus for analyzing an image of an imaged particle, the particle image analyzing apparatus comprising: an illuminating unit for providing dark field illumination the a particle; an imaging unit for acquiring capturing an imaged image by imaging the dark field illuminated particle; and an image processing unit for extracting a particle image from the imaged image captured by the imaging unit, based on a threshold value larger than a luminance value substantially corresponding to the background of the particle image, and analyzing the extracted particle image to obtain morphological feature information indicating the morphological feature of the particle; wherein the image processing unit extracts the particle image from the imaged image based on a threshold value larger than a luminance value substantially corresponding to the background of the particle image.

Abstract: In certain embodiments of the invention, a plurality of images of one or more subjects may be captured using different imaging techniques, such as different modalities of scanning probe microscopy. Parameters may be estimated from the plurality of images, using one or more models of known molecular structures to provide a model-based analysis. The estimated parameters may be fused, with further input from physical models of known molecular structures. The fused parameters may be used to characterize the subjects. Such characterization may include the detection and/or identification of specific molecular structures, such as proteins, peptides and/or nucleic acids of known sequence and/or structure. In some embodiments of the invention the structural characterizations may be used to identify previously unknown properties of a subject molecule.

Abstract: A method of determining an amount of at least one molecular species in a sample from an image of the sample captured by an image acquisition device is provided, each molecular species being indicated by a dye. A dye space representation of a plurality of dyes is formed by orthogonally adding the correspondence tables of the dyes, each correspondence table having a plurality of normalized RGB triplets and incrementally extending from 0% to 100% transmittance. The dye space representation has one dimension for each dye and provides a reference model for a combination of the plurality of dyes. Each pixel of an image of the sample stained with the combination of the plurality of dyes is compared to the reference model, each pixel having a color defined by an RGB triplet, so as to determine an optimal combination of normalized RGB triplets from the respective correspondence tables of the dyes producing the color of the respective pixel.

Abstract: Methods and systems are provided for feature selection in machine learning, in which the features selected for inclusion in a prediction rule are selected based on statistical metric(s) of feature contribution and/or model fitness.

Abstract: A microarray image is segmented into discreet segments for respective spots in the microarray image based on locating microarray image rows and columns by maximizing scores associated with vertical and horizontal image projections. To determine the locations of the rows and columns that extend through artifacts that involve multiple spots and/or multiple columns and rows, the scores may also include contributions from the gaps between adjacent rows and columns. The scores are calculated by stepping windows containing nominally spaced spot-sized row or column boundaries, over the horizontal projection curves. At each step a total row or column score is calculated that represents the areas of the projection curves that fall within the row boundaries. The system then selects the window positions that correspond to the maximum total row score and total column score, and uses the locations of the boundaries as the locations of row and column “stripes” that are sized to the spot diameters.

Abstract: The present invention relates to systems and methods for monitoring the amplification of DNA molecules and the dissociation behavior of the DNA molecules.

Abstract: Combinatorially-synthesized deoxyribonucleic acid (DNA) oligonucleotides attached to encoded beads that are hybridized to amplified and labeled genomic DNA or ribonucleic acid (RNA) are analyzed using a flow imaging system. Oligonucleotides and corresponding reporters are bound to the surfaces of a plurality of small beads such that different beads bear different oligo sequences. Each bead bears a unique optical signature comprising a predefined number of unique reporters, where each reporter comprises a predefined combination of different fluorochromes. The composite spectral signature in turn identifies the unique nucleotide sequence of its attached oligo chains. This optical signature is rapidly decoded using an imaging system to discriminate the different reporters attached to each bead in a flow in regard to color and spatial position on the bead.

Abstract: 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.

Abstract: 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.

Abstract: The present invention provides a unique low cost vision inspection and classification system and methods for automatic inspection and classification of a microarray slide without manual intervention. The method first performs morphological dilation operation several times such that internal microarray spots are merged as a big connected component; then, the orientation of the merged spots, with respect to the X-axis and Y-axis is computed by computing the angle of the external boundaries of the connected component using Sobel XY operators for both edges and orientation determination, or using the moment-based algorithm for direct orientation determination; and the translational offset is determined by finding the X and Y centroids of the connected component. Moreover, the present invention provides threshold methods for classifying spots into normal spots, weak spots, missing spots, or overlapping spots.

Abstract: 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.

Abstract: A method of image analysis applicable to the analysis of arrays, such as DNA or protein microarrays. In the method the luminous spots of the array are filtered and isolated without any intervention of the operator by using a technique of morphological filtering. The spots thus isolated are subsequently analyzed by a fuzzy logic algorithm.

Abstract: 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.

Abstract: 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.

Abstract: The present invention provides a variety of microscale bioreactors (microfermentors) and microscale bioreactor arrays for use in culturing cells. The microfermentors include a vessel for culturing cells and means for providing oxygen to the interior of the vessel at a concentration sufficient to support cell growth, e.g., growth of bacterial cells. Depending on the embodiment, the microfermentor vessel may have various interior volumes less than approximately 1 ml. The microfermentors may include an aeration membrane and optionally a variety of sensing devices. The invention further provides a chamber to contain the microfermentors and microfermentor arrays and to provide environmental control. Certain of the microfermentors include a second chamber that may be used, e.g., to provide oxygen, nutrients, pH control, etc., to the culture vessel and/or to remove metabolites, etc. Various methods of using the microfermentors, e.g., to select optimum cell strains or bioprocess parameters are provided.

Abstract: Nucleic acid microparticles are sequenced by performing a sequencing reaction on the microparticles using one or more reagents, selectively exciting the microparticles in an excitation pattern, optically imaging the microparticles at a resolution insufficient to resolve individual microparticles, and processing the optical images of the microparticles using information on the excitation pattern to determine the presence or absence of the optical signature, which indicates the sequence information of the nucleic acid. An apparatus for optical excitation of the microparticles comprises an optical fiber delivering a first laser beam, and an interference pattern generation module coupled to the optical fiber. The interference pattern generation module splits the first laser beam into second and third laser beams and generates the excitation pattern for selectively exciting the microparticles by interference between the second and third laser beams.

Abstract: An optical measurement device for measurement of chemical and/or biological samples comprises an illumination means (16) for illuminating the sample (20) to be measured. Further, an optics means (22) is provided for imaging a sample area in an image field (10). A first partial area (12) of the image field is covered by a first detector (28), and a second partial area (14) of the image field (10) is covered by a second detector (34). Thus, it is possible to change between two measurement methods without switching or to perform two measurements on a sample at the same time.

Abstract: A method of moving figures whereby a number of aligned figures can be efficiently moved while maintaining the alignment. The method includes a figure group generating step of generating a plurality of figure groups arranged in a matrix by grouping a plurality of figures arranged in a matrix; an overall reference figure setting step of setting an overall reference figure selected from said plurality of figures; an entire figure moving step of moving all of the figures in the same manner as said overall reference figure when said overall reference figure is selected and moved; a reference figure setting step of setting a single reference figure selected from said plurality of figures in each of said figure groups; and a figure group moving step of moving all of the figure groups except for the figure group containing said overall reference figure while maintaining the relative relationships between the rows and columns and between the figure groups, when one of said reference figures is selected and moved.

Abstract: The apparatus and method of the invention provide for assigning coordinates to samples in an array. The method is based on a hierarchical pattern matching to a local lattice structure that is used as a template. Starting from the best local match, the pattern is expanded hierarchically to encompass the entire array.

Abstract: 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.

Abstract: 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.

Abstract: A method for defining a volume of interest (VOI) in a medical image is presented. A user interface is used to select a point on an initial linear border segment of a volume of interest. The user drops the point at a new position and a processor forms a new, non-linear border segment which includes the point. A 3D presentation of the volume of interest is created.

Abstract: Aspects of the present invention describe a method and apparatus for automating quality control for gene expression data. A computer based device receives gene expression data associated with a spectral species and genetic sample in each well of a plate. Gene expression data may be received from a sequence detection instrument performing one or more gene expression related operations for each of the wells of the plate. The computer based device identifies gene expression data determined to have anomalous characteristics according to a set of one or more quality control metrics and may conditionally flag one or more wells of the plate affected by the anomalous characteristics. Filters can then be selectively applied to temporarily or permanently remove the flagged data from subsequent gene expression studies.

Abstract: A method for extracting array elements from an image of an array, the array being contained within a well of a substrate is provided. The method comprises detecting coordinate locations of frequency spectrum peaks in the image by establishing local regions of the image, each local region containing a distinct frequency spectrum peak of the image; determining grid spacing and rotational characteristics of the image by analyzing the detected coordinate locations of the frequency spectrum peaks with a Fourier transform analysis; using the grid spacing and rotational characteristics of the image to generate a well template, the well template accounting for each array element's relative location within the well; and cross-correlating the generated well template with the image of the array to determine matched locations, the cross-correlated well template accounting for each array element's actual coordinate location within the well.

Abstract: The present invention relates to systems and methods for monitoring the amplification of DNA molecules and the dissociation behavior of the DNA molecules.

Abstract: A method and/or system for making determinations regarding samples from biologic sources. A computer implemented method and/or system can be used to automate parts of the analysis.

Abstract: A method of classifying cells into subpopulations using cell classifying data is described. The method comprises receiving and analyzing image data to identify object areas in the image data to determine, for at least one selected first cell, one or more measurements. A first parameter set is derived from the measurements for the first cell, the first parameter set comprising at least one of said one or more measurements. The first set of cells are classified into subpopulations, and identified to produce first identifying data. Cell classifying data for use in classifying a second set of cells into subpopulations is derived from the first parameter set and the first identifying data. A second set of cells is classified into subpopulations on the basis of one or more measurements taken for cells in the second set of cells, by use of the cell classifying data. The parameter sets of cells may be represented as vectors in an n-dimensional space.

Abstract: In a microarray image analysis system, when one of a plurality of statuses is set for a spot of a microarray by the user, the status of a similar spot is automatically determined. In a microarray image, the user determines a status of a spot, the pixel value matrix of an image in a spot region is learned by a neural network, a vertically and horizontally symmetrical image and an image rotated about the center of the region are formed and are learned by the neural network, and the neural network formed by repeating these steps is used for automatically recognizing the status of an undecided spot.

Abstract: Methods, systems and recordable media for accurately reading and identifying high quality signals from a microarray feature. Signals may be identified and used regardless of their geographic/geometric locations and patterns within the feature zone. High quality signals may be read, identified and outputted from a microarray feature in a geometrically independent manner, such that the best quality signals are identified and useable, regardless of the locations or patterns in the region from which the best quality signals are outputted.

Abstract: A system and method is provided that simultaneously or consecutively collects DNA samples and ridge and valley signatures from the same subject during the same collection window that adds value to forensic data collection processes. The collection of the DNA samples and ridge and valley signatures occur during the same collection window to assured the DNA sample and ridge and valley signatures identify the same individual.

Abstract: Computer programs, systems and the like related to processing, segmenting and feature normalizing digital images. The images are of cells and the methods are useful for the detection of malignancy-associated changes (MAC) in cells, which can be used for the detection of cancer. The programs and methods detect cancer in one tissue by detecting MAC in another tissue, such as associated tissues or non-associated tissues. Examples of associated tissues include nipple aspirates or ductal washings to detect breast cancer, and sputum or bronchial lavage to detect lung cancer. Examples of non-associated tissues include buccal mucosa to detect lung or breast cancer.

Abstract: A method for isolating and purifying nucleic acids with an improved recovery yield is provided. A mixed solution containing the nucleic acids, salts, and an organic solvent is contacted with an adsorption support to cause the nucleic acids to be adsorbed on the support. Then, the nucleic acids are desorbed from the support using an elution bugger. At least one compound containing 2 to 10 carbon atoms as selected from the group consisting of aliphatic ether, aliphatic ester, and aliphatic ketone is used as the organic solvent. The method improves the yield of nucleic acids collection, is easy to implement and less susceptible to contamination.

Abstract: A method and system for estimating the background signal over an arbitrarily-sized region of a scanned image of a molecular array, including a background region surrounding the ROI corresponding to the feature. A bit mask is generated, based on a molecular-array, feature-based data set that includes pixel-based intensities and a list of features, including feature coordinates and feature ROI radii, to indicate those pixels in the scanned image of the molecular array corresponding to background, and those pixels in the scanned image of the molecular array corresponding to features and ROIs. An integrated intensity for a background region of arbitrary size and shape can be efficiently determined by selecting pixels within the background region that are indicated to be background pixels in the bit mask.

Abstract: Image analysis methods and apparatus are used for determination of the ploidy of cells. The methods may involve segmenting an image to identify one or more discrete regions occupied by cells or nuclei, determining the presence of a particular ploidy indicator feature within the region(s), and providing a value of the indicator feature to a model that classifies cells' ploidy on the basis of the indicator feature. In some embodiments, the indicator feature is a level of DNA in a cell. In certain embodiments, the method further comprises treating one or more cells with a marker that highlights the ploidy indicator feature. In certain embodiments, the cells are treated prior to producing one or more images of the one or more cells. In certain embodiments, the ploidy indicator feature comprises DNA and the marker co-locates with DNA and provides a signal that is captured in the image. In certain embodiments, the signal comprises a fluorescent emission.

Abstract: A novel functional imaging system for use in the imaging of unrestrained and non-anesthetized small animals or other subjects and a method for acquiring such images and further registering them with anatomical X-ray images previously or subsequently acquired. The apparatus comprises a combination of an IR laser profilometry system and gamma, PET and/or SPECT, imaging system, all mounted on a rotating gantry, that permits simultaneous acquisition of positional and orientational information and functional images of an unrestrained subject that are registered, i.e. integrated, using image processing software to produce a functional image of the subject without the use of restraints or anesthesia. The functional image thus obtained can be registered with a previously or subsequently obtained X-ray CT image of the subject.

Abstract: Feature locations are determined in an array image obtained from reading a chemical array comprising multiple features arranged in a polygon and which array optionally includes sub-arrays within the array. A complete image of the array or a sub-array is presented on a display. Magnified images of corner regions of the displayed complete image are simultaneously presented on the display with the complete image. A user selection of corners for the array or sub-array are received and an array or sub-array actual outline is generated by linearly connecting the user selected corners. The generated actual outline is presented on the magnified image and may also be simultaneously presented on the complete image. Feature locations in the array or sub-array image may be determined based on the actual outline.

Abstract: Technology is disclosed for highly accurate automated execution of processing for alignment of a detection area to a DNA microarray image file and processing for quantitative determination of success/failure of the alignment during DNA microarray analysis. A probe reactive chip used for the technology comprises a substrate; a spot region wherein spots for fixing a probe capable of specifically reacting to a sample marked so as to be optically detectable are formed in a matrix on a surface of the substrate; and a reference pattern area, which is arranged within the spot region or approximate to the spot region, and comprises a plurality of different alignment marks in order to correct misalignment of the spot during analysis of the sample on the surface of the substrate.

Abstract: An improved anomalous shadow detection system enables more reliable and efficient image diagnosis of an image of a suspected anomalous shadow etc. outputted by image output means. The image output means displays values of standard parameters concerning the suspected anomalous shadow and/or certainty of detection of the suspected anomalous shadow together with the image of the detected suspected anomalous shadow.

Abstract: A method of and apparatus for viewing microscopic images include transmitting tiled microscopic images from a server to a client. The client assembles the tiled images into a seamless virtual slide or specimen image and provides tools for manipulating image magnification and viewpoint. The method and apparatus also provides a virtual multi-headed microscope function which allows scattered viewers to simultaneously view and interact with a coherent magnified microscopic image.

Abstract: The apparatus and method of the invention provide for assigning coordinates to samples in an array. The method is based on a hierarchical pattern matching to a local lattice structure that is used as a template. Starting from the best local match, the pattern is expanded hierarchically to encompass the entire array.

Abstract: The invention relates to an image analysis process for measuring the signal on biochips organized into one or several blocks each comprising a large number of spots each composed of at least one probe, the said process being characterized in that it comprises the following steps: a deposit is made with a constant pitch, the spots appearing in the form of a periodic and regular signal; this periodicity property is used to identify the position of the blocks and the spots, this periodicity being searched for on projections of the image in the x and y directions.

Abstract: A medical image is analyzed using an algorithm requiring input parameters. Values of the input parameters are derived from metadata, indicating properties of the medical image. For example, the metadata may indicate the type of image acquisition device or settings used to create the medical image. In another example, the metadata may relate to the patient upon whom the image is based. This allows optimum values to be selected for the parameters.

Abstract: A method of determining an amount of at least one molecular species in a sample from an image of the sample captured by an image acquisition device is provided, each molecular species being indicated by a dye. A dye space representation of a plurality of dyes is formed by orthogonally adding the correspondence tables of the dyes, each correspondence table having a plurality of normalized RGB triplets and incrementally extending from 0% to 100% transmittance. The dye space representation has one dimension for each dye and provides a reference model for a combination of the plurality of dyes. Each pixel of an image of the sample stained with the combination of the plurality of dyes is compared to the reference model, each pixel having a color defined by an RGB triplet, so as to determine an optimal combination of normalized RGB triplets from the respective correspondence tables of the dyes producing the color of the respective pixel.

Abstract: Apparatus and methods for monitoring, analyzing, and/or discriminating molecular species, preferably a biomolecule, within a medium using a multisensor array (MSA) and multivariate processing. Biological compounds such as nucleotides and polynucleotides can be detected and analyzed. A reaction process such as an accumulation cycle of nucleic acids can be monitored, analyzed, and controlled using a multisensor array (MSA) and multivariate processing. Monitoring a biomolecule includes interrogating the medium, and preferably its gas phase, by coupling a sensor responsive to any changes of the medium and or biomolecule and its secondary products when, for example, an amplification reaction is proceeded. It is also a scope of the present invention to use direct detection and monitoring of biomolecular reactions in real-time without radioactive or fluorescent labeling. A preferred application is real-time polymerase chain reaction (PCR) detection.