Patent application number | Description | Published |
20090253163 | ITERATIVE STAINING OF BIOLOGICAL SAMPLES - Automated methods and devices that facilitate iterative staining of biological samples from imaging applications are provided. The methods include the steps of providing a small volume flow cell containing a biological sample, applying a stain to the biological sample, combining at least two precursor reagents to form an activated destaining agent and wherein the activated destaining agent decomposition rate is greater than or similar to the destaining reaction rate, and flowing the destaining agent over the biological sample at a flow rate that is greater than the decomposition rate of the activated destaining agent. The process of staining, combining and flowing may be iteratively repeated. Also disclosed herein are devices for iterative staining of biological samples comprising a flow cell, in fluid communication with a premixer, wherein the volume capacity of the premixer is smaller than about five times the volume capacity of the flow cell. | 10-08-2009 |
20120269418 | ANALYZING THE EXPRESSION OF BIOMARKERS IN CELLS WITH CLUSTERS - A data set of cell profile data is stored. The cell profile data includes multiplexed biometric image data describing the expression of a plurality of biomarkers with respect to a field of view in which individual cells are delineated and segmenting into compartments. Each cell in the field is assigned to a single cluster in a selected set of clusters based on cell similarity; cell similarity is determined based on a plurality of selected cell attributes. The proportion of cells in each cluster is observed. The observed proportions are examined for an association with a diagnosis, a prognosis, or a response derived from a known association of the selected set of clusters with at least one piece of meta-information including a field of view level assessment or a patient-level assessment. | 10-25-2012 |
20120270752 | ANALYZING THE EXPRESSION OF BIOMARKERS IN CELLS WITH MOMENTS - Cell profile data is stored. The cell profile data comprises multiplexed biometric images capturing the expression of a plurality of biomarkers by at least one tissue sample from a patient with respect to at least one field of view. Individual cells are delineated and segmented into compartments. At least one cell feature is calculated based on the cell's expression of each of a plurality of biomarkers. A first moment is calculated for each cell feature. The moments are examined for an association with a diagnosis, a prognosis of a response to treatment of a condition or disease. Apparatus for performing the foregoing steps are disclosed. | 10-25-2012 |
Patent application number | Description | Published |
20140185905 | ANALYZING THE EXPRESSION OF BIOMARKERS IN CELLS WITH CLUSTERS - A data set of cell profile data is stored. The cell profile data includes multiplexed biometric image data describing the expression of a plurality of biomarkers. Cell profile data is generated from tissue samples drawn from a cohort of patients having an assessment related to the commonality. Multiple sets of clusters of similar cells are generated from the data set; the proportion of cells in each cluster is examined for an association with a diagnosis, a prognosis, or a response; and a predictive set of clusters is selected based on model performance. One predictive set of clusters is selected based on a comparison of the performance of at least one model of the plurality of sets of clusters. Display techniques that aid in understanding the characteristics of a cluster are disclosed. | 07-03-2014 |
20140314299 | System and Method for Multiplexed Biomarker Quantitation Using Single Cell Segmentation on Sequentially Stained Tissue - Improved systems and methods for the analysis of digital images are provided. More particularly, the present disclosure provides for improved systems and methods for the analysis of digital images of biological tissue samples. Exemplary embodiments provide for: i) segmenting, ii) grouping, and iii) quantifying molecular protein profiles of individual cells in terms of sub cellular compartments (nuclei, membrane, and cytoplasm). The systems and methods of the present disclosure advantageously perform tissue segmentation at the sub-cellular level to facilitate analyzing, grouping and quantifying protein expression profiles of tissue in tissue sections globally and/or locally. Performing local-global tissue analysis and protein quantification advantageously enables correlation of spatial and molecular configuration of cells with molecular information of different types of cancer. | 10-23-2014 |
20150050650 | METHODS FOR GENERATING AN IMAGE OF A BIOLOGICAL SAMPLE - A method for generating an image of a region of interest in a biological sample comprising the steps of: generating a first image including the region of interest of the biological sample having undergone a first protocol but not a second protocol; and generating a second image including the region of interest of the biological sample after having undergone a second protocol; wherein the region of interest is smaller than said sample. Also provided is a method of analyzing a biological sample, comprising providing an image of the biological sample according to the method for generating an image of a region of interest in a biological sample, and analyzing the biological sample from the image. Further provided are system and kit that comprise the means for executing the novel methods. | 02-19-2015 |
20150065371 | IMMUNOFLUORESCENCE AND FLUORESCENT-BASED NUCLEIC ACID ANALYSIS ON A SIMGLE SAMPLE - A method for providing a composite image of a single biological sample, comprising the steps of generating a first image of the biological sample, generating a second image of the biological sample, and generating a composite image that provides the relative location of both the target protein and the target nucleic acid. Also provided is a method of analyzing a biological sample, comprising providing a composite image of the biological sample according to the method for providing a composite image, and analyzing the expression of the protein and the nucleic acid sequences of interest from the composite image. Further provided are system and kit that comprise the means for executing the novel methods. | 03-05-2015 |
Patent application number | Description | Published |
20110091081 | METHOD AND SYSTEM FOR ANALYZING THE EXPRESSION OF BIOMARKERS IN CELLS IN SITU IN THEIR TISSUE OF ORIGIN - The present application discloses a technique for obtaining and storing data on expression of multiple biomarkers in individual cells or the compartments of individual cells in a tissue specimen and methods of utilizing that data to create groups, the members of which share some degree of similarity greater than the general population from which the data is drawn, by an analysis of digital images of a portion of the tissue specimen which has been iteratively stained to generate optical signals, typically fluorescent, reflective of the amount of each of the biomarkers examined. The analysis of the images involves a segmentation routine whereby each pixel of the examined images is assigned to an individual cell or a compartment of an individual cell, the intensity of the signal representative of each biomarker is measured for each pixel, a dataset is created in which each cell or compartments of each cell is associated with a signal intensity for each biomarker examined, and the dataset is interrogated with appropriate numerical tools to create groups. It also discloses the display of such groups on images of the tissue examined such that the individual cells belonging to a particular group are marked or indicated on one of the images examined. It further discloses examining the biomarker data for each group for possible association with a biological condition or process in cases in which tissue specimens drawn from different subjects or different portions of the tissue of a subject have been examined. It also discloses using this examination in the diagnoses, prognoses or assessment of the response to therapy of a condition or disease. | 04-21-2011 |
20120135449 | ITERATIVE STAINING OF BIOLOGICAL SAMPLES - Automated methods and devices that facilitate iterative staining of biological samples from imaging applications are provided. The methods include the steps of providing a small volume flow cell containing a biological sample, applying a stain to the biological sample, combining at least two precursor reagents to form an activated destaining agent and wherein the activated destaining agent decomposition rate is greater than or similar to the destaining reaction rate, flowing the destaining agent over the biological sample at a flow rate that is greater than the decomposition rate of the activated destaining agent, and releasing the sample from the flow cell wherein the integrity of the sample is intact. The process of staining, combining and flowing may be iteratively repeated. Also disclosed herein are devices for iterative staining of biological samples comprising a flow cell, in fluid communication with a premixer, wherein the volume capacity of the premixer is smaller than about five times the volume capacity of the flow cell. | 05-31-2012 |
20130170728 | PROCESS AND SYSTEM FOR ANALYZING THE EXPRESSION OF BIOMARKERS IN A CELL - The invention relates generally to a process of analyzing and visualizing the expression of biomarkers in an individual cell wherein the cell is examined to develop patterns of expression by using a grouping algorithm, and a system to perform and display the analysis. | 07-04-2013 |
20140024024 | METHODS OF DETECTING DNA, RNA AND PROTEIN IN BIOLOGICAL SAMPLES - Novel methods of probing multiple targets in a biological sample are provide whereby the targets are DNA, RNA and protein. The method comprises subjecting the sample to an in situ hybridization reaction using a labeled nucleic acid probe that binds an RNA target, observing a signal, and optionally removing the signal. The method further comprises an antigen retrieval protocol, observing a signal, removing the signal, and optionally applying a protease treatment to access the sample's DNA targets by subjecting the sample to an in situ hybridization reaction using a labeled nucleic acid probe, observing a signal from the labeled DNA targets, and optionally removing the signal. | 01-23-2014 |