Abstract: Source identification for unknown molecules using mass spectral matching. In an embodiment, a representation of a query mass spectrum is received in a spectrum query. A repository is searched for the query mass spectrum by, for each of a plurality of reference mass spectra, generating a similarity score between the representation of the query mass spectrum and the representation of the reference mass spectrum, when the similarity score exceeds a predetermined threshold value, without utilizing a molecular identity of a molecule represented by the reference mass spectrum, retrieving metadata associated with the reference mass spectrum, and derive context information from the retrieved metadata, and adding the context information to consensus metadata associated with the query mass spectrum, wherein the context information indicates a source of the reference mass spectrum. The consensus metadata is then returned in response to the spectrum query.

Abstract: Methods are provided for efficient training of convoluted neural networks using computer-assisted microscope image acquisition and pre-classification of training images for biological objects of interest. The methods combine use of an automated scanning platform, on-the-fly image analysis parallel to the scanning process, and a user interface for review of the pre-classification performed by the software.

Abstract: A fluorescence image display method and a fluorescence image analyzer capable of suppressing the influence of the operator's skill level and improving the classification accuracy when an operator visually classifies cells is provided. A fluorescence image analyzer, which is an example of an embodiment, includes a light source that irradiates light on a cell having a target site labeled with a fluorescent dye, an imaging unit that acquires a fluorescence image of a cell which emits fluorescence via irradiation by light, and a processing unit that analyzes the fluorescence image by software based on the fluorescence bright spot of the fluorescence image. The processing unit is configured to display a fluorescence image of the cell, the result of the image analysis, and auxiliary information that assists the visual analysis of the fluorescence bright spot included in the fluorescence image.

Abstract: A method for detecting chromosomal abnormalities comprising conversion of a chromosomal image into an ideogram which is compared to a control or standard ideogram of a chromosome; or converting an ideogram of a chromosome into a chromosomal image.

Abstract: A method and device for image registration, and a computer program product. The method includes performing, based on a reference image, a first registration of an image to be registered, including determining a first offset between predetermined areas on the image and the reference image, and moving all bright spots on the image based on the first offset; performing, based on the reference image, a second registration with respect to the first registered image, including merging the first registered image and the reference image, calculating the offset of all overlapped bright spots in the predetermined area on the merged image to determine a second offset, two or more bright spots distanced by less than a predetermined number of pixels being one overlapped bright spot, and moving, on the basis of the second offset, all bright spots on the first registered image, thus implementing the registration of the image.

Abstract: Machine teaching in an embodiment can include receiving a user annotated concept for a given image in given context. The given image can be broken into parts and classified. Relationships can be determined associated with the parts. The created relationships can be stored along with the user annotated concept in a knowledge base. One or more similar images can be annotated using the parts and relationships. A second image associated the given context can be retrieved, decomposed into parts. The parts can be classified. Relationships can be determined associated with the second image's parts. Classifications and relationships associated with the second image's parts can be compared with classifications and relationships associated with the given image's parts. Based on comparing, the second image can be annotated with the user annotated concept for the given image.

Abstract: An integrated module assembly can include: an optical integrated circuit having first and second optical devices; a PCB having first and second holes therein, where the optical integrated circuit is coupled upside down to a first side of the PCB; and first and second lenses coupled to a second side of the PCB, where the first and second sides of the PCB are opposite thereto; and where the first lens is in alignment with the first hole and the first optical device, and the second lens is in alignment with the second hole and the second optical device.

Abstract: An information processing apparatus comprises an extraction part and a genetic information generation part. The extraction part extracts a phenotypic site(s) representing a genetic phenotype(s) of a living entity from the image. The genetic information generation part generates genetic information of the living entity captured in the image based on the phenotypic site(s) extracted by the extraction part. The image comprises a person image in which a person captured. The genetic information generation part may generate genetic information of the person captured in the person image.

Abstract: Provided is an imaging apparatus that includes an irradiation unit that irradiates a subject with light, an imaging unit that images the subject a plurality of times, a control unit that controls the imaging unit and the irradiation unit, and a combination unit that combines a plurality of imaged images obtained by the imaging unit. The imaging unit has a plurality of imaging elements disposed in a matrix when viewed from the side of the subject. The irradiation unit has a plurality of light emitting elements provided so as to correspond to the plurality of imaging elements. The control unit controls the irradiation unit to turn on the plurality of light emitting elements different for each imaging among the plurality of light emitting elements, and controls the imaging unit to drive the plurality of imaging elements corresponding to the plurality of light emitting elements that are not turned on.

Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.

Abstract: Provided herein are methods, compositions, and kits for preparing biological samples for multiplex spatial gene expression and proteomic analysis, such as determining a location of a nucleic acid analyte and a protein analyte in a biological sample.

Abstract: Multiplexed fluorescent imaging which is essential for finding out how various biomolecules are spatially distributed in cells or tissues is disclosed. The present disclosure may obtain 10 or more different biomolecule images with one labeling and imaging by newly designing selection of fluorophores, detection spectral ranges, and signal unmixing algorithm. The present disclosure is a blind unmixing technology for unmixing an image without an emission spectrum of fluorophore, and in this technology, 4 pairs of fluorophores are used, and each pair consists of two fluorophores in which emission spectra are overlapped. Each pair of fluorophores is strongly excited by only one excitation laser. Two images with different detection spectral ranges are obtained for each pair, and two images are unmixed via mutual information minimization without fluorophore emission spectrum information. Two images also may be unmixed via Gram-Schmidt orthogonalization and fluorescence measurement based unmixing.

Abstract: Provided herein are methods and systems for the analysis of biomarkers, and methods of providing diagnoses and/or prognoses therewith. In particular, methods and systems for performing biomarker ratio imaging microscopy (BRIM) are provided, as well as methods of using BRIM for the analysis of biomarker pairs (e.g., CD44/CD24, N-cadherin/E-cadherin, CD74/CD59, etc.) diagnosis and/or prognosis of cancer (e.g., ductal carcinoma in situ).

Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.

Abstract: A method includes: receiving a defect map from a defect scanner, wherein the defect map comprises at least one defect location of a semiconductor workpiece; annotating the defect map with a reference fiducial location of the semiconductor workpiece; determining a detected fiducial location within image data of the semiconductor workpiece; determining an offset correction based on comparing the detected fiducial location with the reference fiducial location; producing a corrected defect map by applying the offset correction to the defect map, wherein the applying the offset correction translocates the at least one defect location; and transferring the corrected defect map to a defect reviewer configured to perform root cause analysis based on the corrected defect map.

Abstract: A method of identifying molecular parameters may include receiving observed transition frequencies, generating transition frequency sets and a spectral parameter sets, training one or more artificial neural networks by analyzing the transition frequency sets and the spectral parameter sets, analyzing the observed transition frequencies using the one or more trained artificial neural networks to predict estimated spectral parameters, and identifying molecular parameters by analyzing the estimated spectral parameters.

Abstract: Methods and compositions for nucleic acid amplification, detection, and genotyping techniques are disclosed. In one embodiment, a nucleic acid molecule having a target-specific primer sequence; an anti-tag sequence 5? of the target-specific primer sequence; a tag sequence 5? of the anti-tag sequence; and a blocker between the anti-tag sequence and the tag sequence is disclosed. Compositions containing such a nucleic acid molecule and methods of using such a nucleic acid molecule are also disclosed.

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a sample of DNA from the mother of the fetus and from the fetus, and from genotypic data from the mother and optionally also from the father. The ploidy state is determined by using a joint distribution model to create a set of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. In an embodiment, the mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias.

Abstract: Disclosed herein are techniques related to automated generation of regular expressions. In some embodiments, a regular expression generator may receive input data comprising one or more character sequences. The regular expression generator may convert character sequences into a sets of regular expression codes and/or span data structures. The regular expression generator may identify a longest common subsequence shared by the sets of regular expression codes and/or spans, and may generate a regular expression based upon the longest common subsequence.

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a sample of DNA from the mother of the fetus and from the fetus, and from genotypic data from the mother and optionally also from the father. The ploidy state is determined by using a joint distribution model to create a set of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. In an embodiment, the mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias.

Abstract: An information processing apparatus comprises an extraction part and a genetic information generation part. The extraction part extracts a phenotypic site(s) representing a genetic phenotype(s) of a living entity from the image. The genetic information generation part generates genetic information of the living entity captured in the image based on the phenotypic site(s) extracted by the extraction part. The image comprises a person image in which a person captured. The genetic information generation part may generate genetic information of the person captured in the person image.

Abstract: The present invention relates to methods of target nucleic acid amplification and uses thereof in methods of sequencing, or other down-stream applications such a genotyping or cloning. More specifically, the methods relate to methods of target nucleic acid amplification through the use of a universal hairpin primer.

Abstract: A classification system and a classification method of the autoantibody immunofluorescence image are disclosed. The system includes an input device, a processor and an output device. The plurality of cell immunofluorescence images and the corresponded extractable nuclear antigen results are input through the input device. The processor conducts a plurality of convolution neural network calculation and output the classification based on the extractable nuclear antigen results, so as to obtain an extractable nuclear antigen classification model. When the autoantibody immunofluorescence image is input by the input device, the corresponded classification of the extractable nuclear antigen can be predicted. The classification result is output through the output device.

Abstract: An image processing apparatus includes: a fluorescence intensity information storage configured to store therein fluorescence intensity information and fluorescence intensity information; and a processor including hardware.

Abstract: Methods, storage mediums, and systems for image data processing are provided. Embodiments for the methods, storage mediums, and systems include configurations to perform one or more of the following steps: background signal measurement, particle identification using classification dye emission and cluster rejection, inter-image alignment, inter-image particle correlation, fluorescence integration of reporter emission, and image plane normalization.

Abstract: A method includes: receiving a defect map from a defect scanner, wherein the defect map comprises at least one defect location of a semiconductor workpiece; annotating the defect map with a reference fiducial location of the semiconductor workpiece; determining a detected fiducial location within image data of the semiconductor workpiece; determining an offset correction based on comparing the detected fiducial location with the reference fiducial location; producing a corrected defect map by applying the offset correction to the defect map, wherein the applying the offset correction translocates the at least one defect location; and transferring the corrected defect map to a defect reviewer configured to perform root cause analysis based on the corrected defect map.

Abstract: A simulate segmentation method of cylinder and pie cake digital models utilizes a three-dimensional model and a reference point to cope with various shapes of the nuclear reactor structures. The segmentation simulation of the nuclear reactor structure is conducted with genetic algorithm. The segmentation simulation of the nuclear reactor structure is achieved by using the genetic algorithm to perform a double selection mechanism on the cross-sectional area of the nuclear reactor structure to select the optimal configuration of the segmentation, thus minimizing the cross-sectional areas of the nuclear reactor structure. The cutter segments the nuclear reactor structure based on the optimal configuration of the segmentation, thereby achieving the purpose of minimizing the attrition rate of a cutter and segmenting the nuclear reactor structure.

Abstract: Improved solid supports and methods for analyzing target nucleotide sequences are provided herein. Certain improvements are directed to efficiently preparing nucleic acids that comprise nucleotide sequences identical to or substantially identical to one or more target nucleotide sequences, or complement thereof. The prepared nucleic acids include a reference sequence that facilitates sequence analysis. The solid supports and methods provided herein minimize the number of steps required by published sequence analysis methodologies, and thereby offer improved sequence analysis efficiency.

Abstract: Involved is a herbicide-resistant protein, coding gene and use thereof. The herbicide-resistant protein comprises: (a) a protein consisting of an amino acid sequence shown in SEQ ID NO: 2; or (b) a protein with the activity of herbicide-resistance which is derived from the amino acid sequence in (a) by replacing and/or deleting and/or adding one or several amino acids in the same. The herbicide-resistant protein of this invention is especially suitable for expression in plants, with broad resistance spectrum to herbicides, especially to phenoxy auxin herbicides.

Abstract: A confocal microscope having a scanning head in the form of a hand piece (102) which may be placed at selected locations on the body of a patient. A laser beam is scanned in orthogonal (horizontal and vertical) directions by scanners (128, 130) which drive scan mirrors (128a, 130a), which are closely adjacent to each other. The optics include an objective lens (138) and a single telescope lens (132, 134). The telescope provides sufficient magnification to overfill the entrance pupil of the objective lens (138) over the entire scan angle produced by the scan mirrors (128a, 130a). The telescope images the entrance pupil of the objective in the beam path between the mirrors of the scanners. Scanner (128) represents a pulse driven resonant scanner (7). The pulse duration is controlled to vary the scan angle and obtain dynamic, electronic image zooming without changing the positional relationship of the telescope lenses.

Abstract: Method and device for capturing images of a target object using image templates at a device are disclosed. The method includes rendering an image template on the display for determining a position of the target object in an image to be captured using the device; capturing a first image of the target object using the image sensor and displaying the captured first image on the display while keeping the image template on the display; extracting one or more features associated with the position of the target object from the captured first image; determining whether the one or more features extracted from the captured first image match the image template; and generating an alert signal in accordance with a determination that at least one of the one or more features extracted from the captured first image matches the image template.

Abstract: Embodiments of a method and/or system of transmitting and/or receiving data is disclosed.

Abstract: A method for analyzing biological reaction systems is provided. The method includes receiving an image of a substrate including a plurality of reaction sites after a biological reaction has taken place. Next, the method includes removing a noise background from the first image. The method includes determining an initial position of each reaction site based on an intensity threshold to generate a initial position set, then refining the initial position set of each reaction site based on an expected pattern of locations of the plurality of reaction sites to generate a first refined position set. The method further includes determining a presence or absence of a fluorescent emission from each reaction site based on the first refined position set and the first image.

Abstract: A method for variant calling in a next generation sequencing analysis pipeline involves obtaining a plurality of sequence reads that each include a nucleotide aligned at a nucleotide position within a sample genome. The method also involves obtaining a plurality of alleles associated with the nucleotide position. The method further involves determining that a particular allele of the plurality of alleles matches one or more sequence reads of the plurality of sequence reads, wherein the particular allele is located at the nucleotide position. Additionally, the method involves generating an image based on information associated with the plurality of sequence reads. Further, the method involves determining, by providing the generated image to a trained neural network, a likelihood that the sample genome contains the particular allele. The method may also involves providing an output signal indicative of the determined likelihood.

Abstract: The present disclosure relates to systems and methods for cell recognition. At least one embodiment relates to a method for recognizing cell. The method includes receiving an image of the cell. The method also includes performing edge detection on the image of the cell. Further, the method includes detecting ridges within the image of the cell. In addition, the method includes quantifying an internal complexity of the cell by gauging a contrast of the ridges with an average of a Laplacian on the detected ridges.

Abstract: A method and corresponding apparatus for identifying tandem repeats in a nucleotide sequence is described. Tandem repeats can be identified by identifying one or more lines present in a self-alignment plot of the nucleotide sequence. The disclosed method includes identifying one or more square-shaped subregions (SSS) representing a tandem repeat and each associated with a plurality of identified candidate alignments by: i) estimating a defining point of an individual square for each of the candidate alignments, each candidate alignment having a start point and an end point, the start point and the end point positioned along adjacent sides of the individual square; ii) selecting one or more seed alignments from the one or more candidate alignments; and iii) associating the one or more candidate alignments with the one or more seed alignments. Based on the associating, a final SSS representing a tandem repeat is determined and its presence is reported.

Abstract: A stand-off optical measuring system based on Raman scattering for detecting and identifying chemical threat substances includes a spectrometer having a dispersive device in front of a 2-dimensional detector, with the entrance of the spectrometer being a coded aperture. The measuring system is configured to be able to quickly adapt to different measuring conditions by the coded aperture being a programmable coded aperture.

Abstract: Improved solid supports and methods for analyzing target nucleotide sequences are provided herein. Certain improvements are directed to efficiently preparing nucleic acids that comprise nucleotide sequences identical to or substantially identical to one or more target nucleotide sequences, or complement thereof. The prepared nucleic acids include a reference sequence that facilitates sequence analysis. The solid supports and methods provided herein minimize the number of steps required by published sequence analysis methodologies, and thereby offer improved sequence analysis efficiency.

Abstract: An ultrasonic diagnostic apparatus (100) that decides a type of a tumor contained in a specimen includes: an image forming unit (103) that forms an ultrasonic image corresponding to an echo signal received from the specimen after administration of a contrast medium; a feature value calculating unit (106) that classifies each of a plurality of pixel regions contained in a tumor region including the tumor in the ultrasonic image into a low-luminance region, or a high-luminance region having higher luminance than the luminance of the low-luminance region, and calculates, based on a difference between a variance at a position of the low-luminance region and a variance at a position of the high-luminance region, a ring level indicating a degree of a ring shape of an image of the tumor region, the ring shape in which a luminance value of a central portion is lower than a luminance value of a peripheral portion surrounding the central portion; and a type deciding unit (107) that decides the type of the tumor based o

Abstract: Embodiments of methods, apparatuses, devices, and/or systems for representing a tree comprising at least a node or at least an edge in the form of signals and/or states, as one or more target numerical signal values substantially in accordance with transformation of the tree to the one or more target numerical signal values based at least in part on an association of trees and numerical signal values are disclosed.

Abstract: A method for analyzing biological reaction systems is provided. The method includes receiving an image of a substrate including a plurality of reaction sites after a biological reaction has taken place. Next, the method includes removing a noise background from the first image. The method includes determining an initial position of each reaction site based on an intensity threshold to generate a initial position set, then refining the initial position set of each reaction site based on an expected pattern of locations of the plurality of reaction sites to generate a first refined position set. The method further includes determining a presence or absence of a fluorescent emission from each reaction site based on the first refined position set and the first image.

Abstract: A multi-well plate reader including an emitter assembly having a plurality of emitters and a receptor assembly including a plurality of receptors separated by at least one spacer element such that a multi-well plate can be inserted between the emitter assembly and the receptor assembly. The emitters and receptors are paired and arranged in parallel arrays such that electromagnetic radiation can be transmitted through each well of the multi-well plate to a corresponding receptor to determine the opacity of the biological material contained within the well. Each well of the multi-well plate can be evaluated by a different emitter receptor pair allowing the entire multi-well plate to be efficiently monitored at a high throughput.

Abstract: A multispectral imaging device includes: an illumination optical system; and an imaging optical system, wherein the illumination optical system includes a filter group disposed in an overlap region of bundles of illumination rays which reach points in an imaging area of a subject, and including at least a first filter and a second filter having different transmission properties, and the imaging optical system includes: an image sensor which includes at least first light receiving elements and second light receiving elements; and a separation optical element which guides light which has passed through the first filter to the first light receiving elements, and guides light which has passed through the second filter to the second light receiving elements.

Abstract: Intelligent multi-scale image parsing determines the optimal size of each observation by an artificial agent at a given point in time while searching for the anatomical landmark. The artificial agent begins searching image data with a coarse field-of-view and iteratively decreases the field-of-view to locate the anatomical landmark. After searching at a coarse field-of view, the artificial agent increases resolution to a finer field-of-view to analyze context and appearance factors to converge on the anatomical landmark. The artificial agent determines applicable context and appearance factors at each effective scale.

Abstract: A cell analysis apparatus includes an optical detection section that accommodates a flow of a measurement sample obtained from a biological sample and a pigment into a flow cell. A light source irradiates the measurement sample flowing in the flow cell and a fluorescence detector detects fluorescence from the measurement sample. A signal processing circuit acquires a value reflecting the height of a waveform of the signal and a value reflecting the length of a ridge line of the waveform of the signal, and a system control section distinguishes between an aggregating cell formed by aggregation of a plurality of cells and a non-aggregating cell, based on the value of the fluorescence signal obtained by the signal processing circuit.

Abstract: An improved diagnostic resolution of digital slide images is obtained by scanning a first digital slide image at diagnostic resolution that is then deconvolved into separate images with one stain per image. The single stain images are then enhanced with image adjustments and/or processed with image analysis algorithms. The resulting single image data sets from the image analysis algorithms can then be stored. Additionally, the resulting enhanced single images can be recombined into a second digital slide image at diagnostic resolution that is also enhanced.

Abstract: A method of sampling feature points, an image matching method using the same, and an image matching processor are disclosed. The method of sampling feature points for image matching includes: dividing a first image into a plurality of regions corresponding to a number of feature points to be sampled; extracting a sampled feature point from each of the regions such that a distance between a sampled feature point of one region and a sampled feature point of another region satisfies a predetermined condition; and estimating a homography on the basis of the extracted sampled feature points and corresponding sampled feature points of a second image to be matched with the first image.

Abstract: A method for determining a media size of a target scanned on the platen of the flatbed scanner using a fiducial placed on a backer of the flatbed scanner at a predetermined location. The fiducial is comprised of a plurality of objects, either placed in a predetermined pattern or randomly within a fiducial frame. A target is placed on the platen of the flatbed scanner and scanned along with the backer. The scanned image data of the target and backer is searched for the fiducial image. When the fiducial image is found, the media is selected to be of a first target type having a first length, and, when the fiducial is not found the target is selected to be of a second target type have a second length longer than the first length.

Abstract: A list of elements in a set of elements is matched by means of regular expressions that define respective groups of elements in the set by approximately matching by means of the regular expressions the list of elements by locating recurrences of the regular expressions in the list of elements with a maximum number of matching errors. The matching errors correspond to insertions deriving from the superposition of groups of elements related to different regular expressions. Each time the recurrence of one regular expression is located in the list, the group of elements defined by the regular expression thus located is removed from the list, while leaving in the list those elements corresponding to errors. The approximate matching can be performed by representing each regular expression in terms of Glushkov automata. The method is applicable, e.g.

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 interference pattern generation module that splits a 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.