Abstract: A method for fixing a biological sample includes delivering energy through a biological sample that has been removed from a subject, while fixing the biological sample. A change in speed of the energy traveling through the biological sample is evaluated to monitor the progress of the fixation. A system for performing the method can include a transmitter that outputs the energy and a receiver configured to detect the transmitted energy. A computing device can evaluate the speed of the energy based on signals from the receiver.

Abstract: A method of processing droplets in a microfluidic system. The method may comprise capturing a time sequence of images of a droplet as it passes through a channel in a microfluidic system. The method may further comprise processing each image of the sequence of images using a convolutional neural network to count a number of cells or other entities visible in each image the droplet. The method may further comprise processing the count of the number of cells or other entities visible in each image of the droplet to determine an estimated number of cells or other entities in the droplet. The method/system may further comprise controlling a microfluidic process performed on the droplet responsive to the estimated number of cells or other entities in the droplet. Implementations of the method use the changing orientation and disposition of droplet contents in combination with machine learning to improve monoclonality assurance.

Abstract: The present invention relates to systems and methods for tissue processing and analysis. Tissue chambers are configured to allow single-container chemical processing, imaging, and wax embedding of tissue samples in a single container without manipulation between steps. Tissue chambers with features to support the tissue sample and allow fluid flow between the tissue sample and the tissue chamber surface are disclosed. The features may be index matched to sample structures of interest or dissolvable in clearing solution to allow for in-chamber imaging with minimal distortion. Specialized tissue processing and wax removal apparatuses are also disclosed including for use with tissue chambers having frangible portions to permit ease of wax removal.

Abstract: A method and system are described for processing tissues according to particular processing protocols that are established based on time-of-flight measurements as a processing fluid is diffused into a tissue sample. In one embodiment, measurement of the time it takes about 70% ethanol to diffuse into a tissue sample is used to predict the time it will take to diffuse other processing fluids into the same or similar tissue samples. Advantageously, the disclosed method and system can reduce overall processing times and help ensure that only samples that require similar processing conditions are batched together.

Abstract: The method includes fixing the tissue sample with a first fixation solution immersing the tissue sample in a delipidation solution including a chaotropic agent configured to induce a swelling of the sample; staining the tissue sample; dehydrating the tissue sample in an organic dehydration solution, the dehydration solution configured to induce a shrinking of the sample; and immersing the fixed tissue sample in an organic clearing solution.

Abstract: A portable variable focus microscope includes a housing having a lower section and an upper section secured together. A lens is removably disposed on at least one lens retention feature of the upper section. The scope further includes a slide platform and a height adjuster, where rotation of the height adjuster within the scope housing adjusts a relative distance between the slide platform and the lens to adjust a focus of the lens. The scope may be used in conjunction with a mobile data device to capture an image of a sample on a slide received in the scope. A program including a CNN algorithm may be employed to identify contaminants in the sample.

Abstract: The invention relates to a method for use in characterizing lesions in radiology images, comprising performing a computer-based analysis of a pathology image of a sample of a lesion of a subject in order to recognize tissue and/or cellular characteristics of the lesion, wherein the analysis produces a derived pathology image that represents the recognized tissue and/or cellular characteristics, computing one or more radiology features for the lesion from a radiology image of the lesion, and determining correlations between the computed one or more radiology features and the recognized tissue and/or cellular characteristics. With this method, biological ground truth information can be used to identify radiology features that are indicative of certain tissue and/or cellular characteristics of lesions and that may therefore be better suited for characterizing the lesions.

Abstract: Methods and systems for automating and managing efficient workflow for the viewing and analysis of diagnostic images within a healthcare enterprise network generate virtual worklists listing of healthcare data orders allocated to a specific destination. The methods and systems can provide flexible worklist viewing, system administration, and maximized diagnostic throughput.

Abstract: An apparatus attaches to a microscope slide to form an enclosed fluidic chamber with input and output ports, where a tissue or cell sample on the slide can be processed using techniques such as immunohistochemical staining. Flow of reagents within the chamber can be laminar and highly uniform across the sample surface to achieve staining that is free of gradients. The sample can be imaged prior to, during, or after any given processing step. Methods for staining and imaging a sample can be implemented through one or more rounds of labeling, label removal or erasure and imaging. Samples can be imaged many times to achieve very high multiplexing levels. Samples can be placed on an imaging apparatus at various times and removed from the imaging apparatus for certain steps.

Abstract: This application provides a pathological section image processing method performed by a computer device. The method includes: obtaining stained images of a pathological section after cell membrane staining; determining cell nucleus positions of cancer cells in a stained image under an ith field of view in the n fields of view; generating a cell membrane description result of the stained image under the ith field of view, the cell membrane description result being used for indicating completeness and staining intensity of the cell membrane staining; determining quantities of cells of types in the stained image under the ith field of view according to the cell nucleus positions and the cell membrane description result; and determining an analysis result of the pathological section according to quantities of the cells of types in the stained images under the n fields of view.

Abstract: A specimen support tool for supporting a slice prepared by using a microtome includes a specimen support member on which a groove for guiding the slice is formed.

Abstract: In flow cytometry, particles (2) can be distinguished between populations (8) by combining n-dimensional parameter data, which may be derived from signal data from a particle, to mathematically achieve numerical results representative of an alteration (48). An alteration may include a rotational alteration, a scaled alteration, or perhaps even a translational alteration. Alterations may enhance separation of data points which may provide real-time classification (49) of signal data corresponding to individual particles into one of at least two populations.

Abstract: The present disclosure discusses a method of separating a sample including oligonucleotides including coating a flow path of a chromatographic system; injecting the sample comprising oligonucleotides into the chromatographic system; flowing the sample through the chromatographic system; and separating the oligonucleotides. In some examples, the coating of the flow path is non-binding with respect to the analyte, such as oligonucleotides. Consequently, the analyte does not bind to the coating of the flow path. The non-binding coating eliminates the need for passivation, which can eliminate the formerly needed time to passivate as well. In addition, analyte can be recovered with a first injection in a system, such as chromatographic system.

Abstract: A method for laser microdissection includes: processing a microscopic examination object by a laser beam using tuples of coordinate values which respectively indicate positions of target points on the examination object at least in a first spatial direction and a second spatial direction orthogonal to the first spatial direction, positions of at least three reference points being ascertained beforehand in each case in the first and second spatial directions and also in a third spatial direction orthogonal to the first and second spatial directions; defining a reference plane based on the positions of the reference points; and determining, for the target points, further coordinate values indicating an expected position of the target points on the examination object in the third spatial direction in each case, as determined further coordinate values, the determining of the further coordinate values being performed depending on the defined reference plane.

Abstract: The present invention relates a simple method for evaluating free eukaryotic cell nuclei for biomarkers of DNA damage and/or transcription factor activation, activity, or expression levels and/or epigenetic modifications to chromatin or chromatin-associated factors. The invention also teaches useful strategies for combining nuclear biomarkers into a matrix of endpoints that are capable of elucidating genotoxicants' primary mode of DNA-damaging activity. Kits for conducting methods according to the invention are also described.

Abstract: A system and method for interpolating soil chemistry variables to different plots of land is described. A first interpolation training model includes a machine learning model that receives soil composition information. A distance field training model generates spatial predictors that are applied to the machine learning model. The first interpolation training model prioritizes spatial smoothing over accuracy. A second interpolation training model is also applied that includes a distance weighting training model that more greatly weighs interpolated soil composition information closer to a point of interpolation than interpolated soil composition information that is further away to the point of interpolation. The second interpolation training model prioritizes accuracy over spatial smoothing. The illustrative crop prediction engine estimates soil chemistry values at different locations with the first interpolation training model and the second interpolation training model.

Abstract: The present invention relates to a method for determining the three dimensional structure of biomolecules, such as proteins, protein fragments, and peptides. The biomolecule is encapsulated in an amorphous silica matrix, from which a needle specimen is prepared. Atom probe tomography is then used to analyze the needle specimen and the data is used to reconstruct the three dimensional structure of the biomolecule. The present invention greatly facilitates determination of the three dimensional structure of biomolecules.

Abstract: A holder system for a scanning probe microscope, including a holder and a fixer. The holder includes a holder top surface, and a holder sidewall. The holder top surface is configured to hold a sample. The holder sidewall extends from the holder top surface. The fixer includes a fixer fixing portion, and a fixer connecting portion. The fixer fixing portion is configured to affix the sample to the holder top surface. The fixer connecting portion is connected to the fixer fixing portion, and is affixed to the holder sidewall. An area to-be-tested of the sample is exposed to the fixer fixing portion.

Abstract: A method is disclosed that permits calculation of reagent concentrations (in SI units) over time and space within a tissue sample as the sample is immersed in the reagent and the reagent diffuses into the tissue sample. The disclosed method has yielded the surprising result that once a formaldehyde concentration at all points within a tissue sample exceeds about 90 mM during a cold step of a cold+hot fixation protocol, the hot step of the fixation protocol can be commenced to provide reliable detection of molecular targets and preservation of tissue morphology in downstream analyses.

Abstract: A method and system are described for processing tissues according to particular processing protocols that are established based on time-of-flight measurements as a processing fluid is diffused into a tissue sample. In one embodiment, measurement of the time it takes about 70% ethanol to diffuse into a tissue sample is used to predict the time it will take to diffuse other processing fluids into the same or similar tissue samples. Advantageously, the disclosed method and system can reduce overall processing times and help ensure that only samples that require similar processing conditions are batched together.

Abstract: A system and method for predicting a crop yield for a type of seed in a location is described. The method includes receiving, at a client device, seasonal crop data for the type of seed, soil data associated with the location, and mapping data associated with the location. The soil data includes soil variables, and the location is represented by voxels. The seasonal crop data, the soil data and the mapping data are uploaded to a geospatial database associated with a crop prediction engine. A random forest prediction model is applied to the seasonal crop data, the soil data and mapping data in the geospatial database by the crop prediction engine, which then ranks covariates to determine one or more significant covariates. The crop prediction engine then re-applies the significant covariates to the random forest prediction model to predict the crop yield for the type of seed at the location.

Abstract: It is aimed to provide a technology that enables highly accurate device performance evaluation and device adjustment in optical analysis of microparticles, using the same type of beads. The present technology provides an information processing device including an information processing unit that acquires a plurality of fluorescence intensities at a plurality of light irradiation powers for a fluorescence signal from a sample including particles labeled with a fluorescent dye having a single fluorescence intensity, recognizes an intensity range of each of the plurality of fluorescence intensities detected on the basis of a fluorescence intensity balance of the sample, and calculates information relating to sensitivity of a fluorescence detection unit.

Abstract: Methods and systems for automating and managing efficient workflow for the viewing and analysis of diagnostic images within a healthcare enterprise network generate virtual worklists listing of healthcare data orders allocated to a specific destination. The methods and systems can provide flexible worklist viewing, system administration, and maximized diagnostic throughput.

Abstract: A system for characterizing at least one particle from a fluid sample is disclosed. The system includes a filter disposed upstream of an outlet, and a luminaire configured to illuminate the at least one particle at an oblique angle. An imaging device is configured to capture and process images of the illuminated at least one particle as it rests on the filter for characterizing the at least one particle. A system for characterizing at least one particle using bright field illumination is also disclosed. A method for characterizing particulates in a fluid sample using at least one of oblique angle and bright field illumination is also disclosed.

Abstract: A system and method for detecting pathogenetic analytes including exciting a large target input area with radiation to produce scattered light to form an input beam, reformatting, with an optical slicer system, the input beam to produce an output beam, dispersing the output beam to produce an output area, capturing excitation data from the output area; and determining, with a processor, a presence of a particular analyte in the input area based on the excitation data. The input area can be greater than 100 micron squared and less than one million microns squared. The optical slicer system can be a high throughput virtual slit system. SERS analysis detects analytes of interest with both high resolution and sensitivity simultaneously, and is applicable for detection of the presence of viruses.

Abstract: A device for taking and optionally processing a sample, includes (i) a housing containing a porous matrix that can receive the sample, (ii) a stopper that can be connected to the housing in a tight manner and including a piston that ensures the tight closing of the housing, compressing the porous matrix or the sample, and (iii) a storage receptacle that can be connected to the housing, can receive the sample that has passed through the porous matrix, and includes at least one conduit connecting the inside of the receptacle to the outside, once the porous matrix or the sample is compressed. The device also includes a seal between the stopper and the storage receptacle. The stopper closes the storage receptacle in a tight manner when the stopper and the storage receptacle are connected to the housing.

Abstract: The present invention relates to a composition for immunostaining cleared large tissues and a method for immunostaining cleared large biological tissues using the same. The composition for immunostaining cleared large tissues increases antibody permeability in cleared biological tissues, in particular, large biological tissues having a thickness of 3 mm or more, to allow antibodies to penetrate deep into thick tissues, thereby overcoming immunostaining problems associated with limited permeation of antibodies in existing methods, reduces the time required for immunostaining large tissues, thereby enabling simple and rapid three-dimensional bioimaging with high resolution for large biological tissues, and may be beneficially used, through structure images, for identifying the causes of various diseases, developing new treatment methods, and predicting the efficacy and toxicity of drugs.

Abstract: An image capturing system includes a camera unit that captures an image of a cell; a display unit; an input unit that receives input from an operator regarding a selection operation on the cell; an analyzing unit that analyzes the image corresponding to the cell to which the selection operation is given and extracts a feature amount of the cell; and a specifying unit that specifies a recommended cell. The specifying unit sets a parameter that defines a range of the cell to be selected based on the feature amount of the cell to which the selection operation is given up to a first time point. In an image including the cell obtained by image capturing at a second time point later than the first time point, the specifying unit specifies the recommended cell on which the operator is prompted to make a selection based on the parameter.

Abstract: A method determines a calibration specification specifying a functional correlation between an NMR measurement variable, determined using an NMR measuring device, for a material to be analyzed and a humidity contained in the material to be analyzed. The method includes provision of a relaxation curve of the material having a known humidity; determination of a relaxation time distribution from the relaxation curve provided; and determination of an approximate relaxation time distribution relative to at least one other humidity. The at least one other humidity is less than the known humidity.

Abstract: A system and a method for unveiling poorly visible or lightly colored nuclei in an input image are disclosed. An input image is fed to a color deconvolution module for deconvolution into two color channels that are processed separately before being combined. The input image is deconvolved into two separate images: a stain image and a counter stain image. A complement of the stain image is generated in order to clearly reflect the locations of the poorly visible or light-colored nuclei. The complement image and the counter stain image are optionally normalized and then combined and segmented, to generate an output image with clearly defined nuclei. Alternatively, the complement of the stain image and the counter stain image can optionally be normalized, and then segmented prior to being combined to generate the output image.

Abstract: The present invention relates to an apparatus (10) for determining cellular composition in one or more tissue sample microscopic images. It is described to provide (210) first image data of at least one tissue sample. The first image data relates to a non-specific staining of a tissue sample of the at least one tissue sample. Second image data of the at least one tissue sample is provided (220). The second image data relates to specific staining of a tissue sample of the at least one tissue sample. Either (i) the tissue sample that has undergone specific staining is the same as the tissue sample that has undergone non-specific staining, or (ii) the tissue sample that has undergone specific staining is different to the tissue sample that has undergone non-specific staining. A non-specific cellular composition cell density map is determined (230) on the basis of the first image data. A specific cellular composition cell density map is determined (240) on the basis of the second image data.

Abstract: The present invention relates a simple method for evaluating free eukaryotic cell nuclei for biomarkers of DNA damage and/or transcription factor activation, activity, or expression levels and/or epigenetic modifications to chromatin or chromatin-associated factors. The invention also teaches useful strategies for combining nuclear biomarkers into a matrix of endpoints that are capable of elucidating genotoxicants' primary mode of DNA-damaging activity. Kits for conducting methods according to the invention are also described.

Abstract: Described herein are computer-implemented methods for analysis of a tissue sample. An example method includes: annotating the whole tumor regions or set of tumorous sub-regions either on a biomarker image or an H&E image (e.g. from an adjacent serial section of the biomarker image); registering at least a portion of the biomarker image to the H&E image; detecting different cellular and regional tissue structures within the registered H&E image; computing a probability map based on the different detected structures within the registered H&E image; deriving nuclear metrics from each of the biomarker and H&E images; deriving probability metrics from the probability map; and classifying tumor nuclei in the biomarker image based on the computed nuclear and probability metrics.

Abstract: The present invention provides a nanoparticle containing a hydrophobic fluorescent substance accumulated therein and a thermosetting resin as a matrix, which nanoparticle, when used for labeling of a biological substance such as a protein or nucleic acid, has brightness sufficient for allowing pathological diagnosis using a fluorescence image obtained thereby. The present invention is a phosphor integrated dots nanoparticles wherein a thermosetting resin contains a structural unit formed from a raw material containing a hydrophobic substituent, and wherein a fluorescent substance is accumulated in the nanoparticle at least by hydrophobic interaction, preferably further by stacking interaction, with the hydrophobic substituent of the thermosetting resin.

Abstract: Implementations of the present invention relate to apparatuses, systems, and methods for constructing and using a metastatic mimetic device. The device includes at least one chamber with a gate structure that allows a channel to selectively allow fluid communication between an interior of the chamber and an exterior of the chamber. The channel includes a porous member extending across a cross-section of the channel to control flow rates or allow the mimetic device to replicate transport across a member.

Abstract: An image processing system configured to receive a first fluorescence image generically indicating the presence of biological matter; transform the first image into a transformed first image having a first color; for each of the biomarkers, receive a respective second fluorescence image indicating signals emitted by fluorescence stain selectively staining the biomarker, transforming the second images into a respective transformed second images having a respective second color; overlaying and combining the transformed first and second images; storing and/or displaying the combined image as the simulated digital bright field IHC or ISH image. The first image is created using an autofluorescence reference spectrum of the tissue sample or of a similar tissue sample or by using a fluorescence reference spectrum of a first stain which generically binds to biological matter of the tissue sample for spectrally unmixing of a multi-spectral digital image of the tissue sample.

Abstract: The present invention relates to a method for detecting cell death using a luminescent compound; to the luminescent compounds for particular uses; to a kit comprising said compounds and to a protein. The method is applicable for detecting cell death, essentially regardless of the mechanism through which cell death occurred or is occurring and is therefore not limited e.g. to detecting cell death resulting from only one mechanism selected from apoptosis and necrosis.

Abstract: An imaging system may include a sample stage having a surface to support a sample to be scanned by the imaging system; an optical stage having an objective lens, the optical stage being positionable relative to the sample stage; an actuator physically coupled to at least one of the sample stage and the optical stage to move the sample stage relative to the optical stage; a servo circuit to control the actuator; a first set of control parameters to control the servo circuit; a second set of control parameters to control the servo circuit; and a servo control circuit to apply the first set of control parameters to the servo circuit when the imaging system is operating in a first mode of operation and to apply the second set of control parameters to the servo circuit when the imaging system is operating in a second mode of operation.

Abstract: The present invention relates a simple method for evaluating free eukaryotic cell nuclei for biomarkers of DNA damage and/or transcription factor activation, activity, or expression levels and/or epigenetic modifications to chromatin or chromatin-associated factors. The invention also teaches useful strategies for combining nuclear biomarkers into a matrix of endpoints that are capable of elucidating genotoxicants' primary mode of DNA-damaging activity. Kits for conducting methods according to the invention are also described.

Abstract: A method for in-vivo cancer diagnosis within a living tissue. The method includes preparing an electrochemical probe by fabricating three integrated electrodes via coating a layer of vertically aligned multi-walled carbon nanotubes (VAMWCNTs) on tips of three electrically conductive biocompatible needles, putting the tips of the three integrated electrodes in contact with a portion of the living tissue by inserting the tips of the three integrated electrodes into the portion of the living tissue, recording an electrochemical response from the portion of the living tissue, where the electrochemical response may include a cyclic voltammetry (CV) diagram with an oxidation current peak corresponding to a hypoxic glycolysis chemical reaction in biological cells within the portion of the living tissue, and detecting a cancer-involving status of the portion of the living tissue based on the oxidation current peak.

Abstract: Single-stranded oligonucleotide probes, systems, kits and methods for chromosome enumeration, gene copy enumeration, or tissue diagnostics. The probes are particularly suited for detecting gene amplification, deletion, or rearrangement in tissue samples in a single, dual, or multiplexed assay. The probes exhibit improved performance compared to industry leading dual-stranded probes; particularly in terms of the rate of hybridization.

Abstract: Systems and methods for automated analysis of histochemical or cytological samples stained for analytes having complex staining patterns are presented. Analyte staining of a biological compartment in a region is quantified, in which said staining is intermixed with analyte staining of an analytically-distinct biological compartment. The systems and methods further include identifying membrane staining of an analyte of interest in regions where diffuse membrane staining is intermixed with cytoplasmic staining and/or punctate staining is disclosed. The systems and methods further include quantifying membrane staining of an analyte of interest in tissue or cytological samples having regions in which membrane staining is intermixed with cytoplasmic staining and/or punctate staining.

Abstract: The present invention provides a stabilized hypohalous acid solution (or formulation thereof), which may be conveniently packaged for sale, or stored for later use on demand. The invention further provides methods of making the stabilized hypohalous acid solutions, as well as methods of use for disinfecting mammalian tissue, including wounds and burns, and treating skin irritations, among other uses.

Abstract: A microscope slide mounting system includes a slide mounting medium, with a predetermined weight of powdered gum arabic in a predetermined weight of distilled water; a predetermined weight of anhydrous chloral; a predetermined weight of anhydrous glycerin; and a predetermined percentage of ethylene glycol; the ethylene glycol acts as a denaturant in the mounting medium; and the ethylene glycol causes mild illness when ingested, thereby discouraging the use of the mounting medium as a sedative or recreational drug and prevents the crystallization of the medium.

Abstract: A clearing agent and mounting solution for microscopy is disclosed comprising at least trichloroethanol and/or derivatives thereof, where the refractive index of the solution is greater than or equal to about 1.3810. Also disclosed are methods of preparing specimens for microscopy.

Abstract: Cell sorting methods that improve sorting efficiency and productivity by elevating sorting pressures and incorporate certain steps to help the cells better survive such elevated pressures. In the case of sperm, sorting the steps of standardizing sperm samples, staining sperm samples in a single step, calibrating a flow cytometer to place sperm in the leading edge of droplets, and changing a catch fluid distance may be incorporated individually, or in combination to help sperm better survive the sex sorting process.

Abstract: A system for generating image-based patient profiles acquires digital images from tissue samples and CT and MRI scans. The system detects objects within the images, measures values related to the detected objects, and displays the measured values in patient profile lists that indicate the normal ranges for measured values. The system indicates which measured values fall outside the normal ranges and navigates the user to the objects in the images associated with the abnormal values when the user selects a measured value in the patient profile. Various risks of the existence of different diseases and the probability of success of specific treatments are displayed on a graphical user interface. The system searches for patterns in the patient data and profile lists that reflect those specific risks and success probabilities. A high probability of disease risk or of the success of a specific treatment is indicated on the graphical user interface.

Abstract: Paraffin-embedded tissue, which may be disposed on a solid substrate, is prepared by a dry technique that removes paraffin from tissue without adding any liquid to the tissue, thereby rendering the tissue substantially free of paraffin. The dry technique may entail applying heat energy to the tissue effective to melt the paraffin and thereby render it flowable, and applying an electric field. The electric field is effective to impart electrical charge to the paraffin and to move the paraffin out from the tissue due to electrical charge repulsion or attraction, which may be assisted by moving an electrode utilized to generate the electric field relative to the paraffin. The electric field, or both the electric field and the heat energy, may be applied until the tissue is substantially free of paraffin.

Abstract: A method of removing a floatation liquid from between a microscope slide and a paraffin embedded biological specimen including position the microscope slide with the paraffin embedded biological specimen floated thereon onto a slide support element. The slide support element is rotated to cause the microscope slide and the paraffin embedded biological specimen to move in a way that causes the floatation liquid disposed between the microscope slide and the paraffin embedded biological specimen to be removed from between the microscope slide and the paraffin embedded biological specimen.

Abstract: A tissue area detection method in digital pathology imaging uses an automated method to detect tissue area of interest (AOI detection) on a Whole Slide Analysis (WSA) or Tissue Micro Array (TMA) thumbnail image. The present method may use preprocessing of the image followed by a two-pass segmentation technique for separating tissue areas from non-tissue areas. The present method may further use global and local window statistics for thresholding to overcome variations in staining intensity that may hamper accurate selection of the area of interest. The present method may also have a classifying process of the tissue area based on the staining method used and applying stain specific filters to remove unwanted artifacts.