Leland Stanford Junior University

Other

David R Parks

Wayne A Moore

Leonore A Herzenberg

Stephen W Meehan

Guenther Walther

Leonard A Herzenberg

Darya Y Orlova

Vernon T Oi

Tom Nozaki, Jr

Richard T Stovel

Ilana Belitskaya-Levy

Jinhui Pan

Richard G Sweet

Mario Roederer

Martin Bigos

Mark Musen

Andrei Vitalievich Chernyshev

Alexander E Moskalensky

Adam S Treister

Gary Breitbard

Virginia M Bryan

Connor Meehan

Connor G W Meehan

James Tung

Some embodiments provide methods, systems and computer-readable media that employ adaptive binning and dissimilarity scores based on a quadratic form distance for multidimensional data for matching clusters in data corresponding to different sample. Some embodiments provide methods, systems and computer-readable media for rendering a first interactive display including a two-dimensional plot of at least a portion of a multidimensional data set and a corresponding second interactive display including a plurality of single parameter charts or histograms, each displaying information corresponding to one-dimensional measurements of a different parameter in the multidimensional data set.

Systems and methods for cluster matching across samples and guided visualization of multidimensional cytometry data

The described invention provides a method and/or system for analyzing data using population clustering through density based merging, and a method for guiding clustering strategy through entropy-based ranking score.

Cluster processing and ranking methods including methods applicable to clusters developed through density based merging

The described invention provides a method for quantifying cellular antigens that is independent of specially prepared calibration beads and antibody reagents. The described method can be applied to both low and high affinity antibodies, under both saturating and non-saturating binding conditions.

Quantification of antigen molecules using dynamic flow cytometry

A method and/or system for analyzing data using population clustering through density based merging.

Method for identifying clusters of fluorescence-activated cell sorting data points

The invention provides a system and method for selecting an optimal multimarker reagent combination for the identification and/or quantification of molecules in or on cells with or without reference to fluorescence or other properties of at least one fluorescent dye or other instrument-measurable atom or molecule associated directly or indirectly with the reagent combination. The method includes specifying, using a computer, a plurality of markers to be detected by a plurality of reagents, generating, using a computer, a plurality of reagent combinations comprising the plurality of reagents to detect the plurality of markers, wherein the reagent combinations are ranked according to at least one user-defined or system-defined criterion, and selecting the optimal reagent combination or providing a rank-ordered list of combinations.

System and method for selecting a multiparameter reagent combination and for automated fluorescence compensation

Disclosed is a method and system for archiving data. A server computer (or any computing device) receives data transmitted over a network from a client computer, wherein at least some of the data was previously collected by a scientific instrument during an experiment. After receiving the data, the server computer updates (e.g., creates) an index for the received data, archives the received data, and automatically transmits a notification to the client computer that the received data has been archived.

Method and system for data archiving

Method for clustering data items through distance-merging and density-merging techniques

This invention relates to the field of flow cytometry. It provides methods for identifying important dye-detector spectral overlaps for use in designing flow cytometry experiments. It further provides methods for quantifying the impact of spectral overlaps on dye selection and detector selection, the methods including the steps of: a) obtaining spectra of a dye; b) obtaining a laser configuration and an optical filter configuration of a detector; c) obtaining a spectrum yield value; and d) ranking the spectrum yield value.

Method for pre-identification of spectral overlaps within fluorescent dye and detector combinations used in flow cytometry

The present invention is related to databases and the exchange of scientific information. Specifically the invention disclosed a unified scientific database that allows researchers to easily share their data with other researches. The present invention also allows for the ease of data collection, annotation, storage, management, retrieval and analysis of scientific data through and into the database. In addition, it allows for archival storage and retrieval of data collected directly from laboratory instruments to ensure data consistency for patent and other purposes. It also allows for ease of sharing data between laboratories in remote locations. The present invention also supports the automated creation of experimental protocols.

Internet-linked system for directory protocol based data storage, retrieval and analysis

The present invention is related to databases and the exchange of scientific information. Specifically the invention discloses a laboratory data management system including a knowledge base that stores characteristics of laboratory reagents, experiment subjects, tissues and cells. The invention also includes an experiment input module that accepts input of parameters of an experiment and data from a knowledge base module. Further, the invention includes a protocol creator connected to the knowledge base module and the experiment input module that creates a laboratory protocol for an experiment based on data supplied from the knowledge base module and the experiment input module. The invention also includes methods to use the described system.

System and method for internet-accessible tools and knowledge base for protocol design, metadata capture and laboratory experiment management

The present invention provides methods of analyzing and/or displaying data. In one aspect, the invention provides methods for visualizing or displaying high dynamic range data obtained from flow cytometry analyses. Related systems and computer programs products are also provided.

Methods and systems for data analysis

This invention relates a series of methods for the visual representation and subsequent application of analyses on complex data sets. In particular, this invention is useful for the analysis of multiple sample sets that share common features, for which similar types of analyses are desired. Three concepts are embodied to aid in this analysis: &ldquo;Functional equivalence by Algorithmic Polymorphism&rdquo; (FEAP), in which an analysis algorithm is abstracted through the use of an associated name; a genealogical metaphor for the representation of successive or parallel analysis steps, in which &ldquo;families&rdquo; of analyses can be easily copied between different sample data sets; and batch analysis through the creation of multi-sample analysis surrogates (MSAS), which are groups of samples wherein analyses applied to an MSAS is then applied to every sample within the MSAS group. This invention has particular utility in the analysis of data derived from flow cytometers, the analysis of complex demographic data, and other similar data sets.

Methods for analysis of large sets of multiparameter data

A system for characterizing objects to be sorted in real time and making sorting decisions using lasers to excite fluorescing dyes used to tag objects such as cells which flow through the laser beam in a stream of conductive fluid. The scattered light and fluorescent light at various frequencies define a multidimensional space. These light characteristics are sensed and digitized. The data so gathered is buffered and then compared to a binary classification tree. The individual parameters cause a certain path through the binary decision tree to be taken while the cell is passing from the point in the stream where the light characteristics are gathered to a point where electrostatically charged electrodes deflect individual statically charged drops containing cells to be sorted into various sorting bins. When the decision tree has been traversed, the sorting decision for the drop containing the cell which had those parameters is done. This sorting decision is buffered until the time the drop reaches the charged electrodes. The sort decision is then accessed and used to properly charge the electrodes so that the drop is diverted into the proper bin.

Apparatus and method for multidimensional characterization of objects in

Method and apparatus for sorting individual particles into containers, such as the wells of a microculture tray, are disclosed. The particles may comprise, for example, individual biological cells which then may be cultured, cloned, analyzed, or the like. The particles are incorporated into a flow stream which is jetted from a nozzle which is vibrated in the direction of the stream to break the jet stream into discrete drops. A particle sensor senses particles in the stream, and a signal processor in response to the particle sensor output produces an output when the sensed particle is of the type to be sorted from the stream. A pulse charger, responsive to the signal processor, is included for charging the drops as they break from the vibrating jet stream. The drops pass between charged deflection plates where they are deflected an amount related to the drop charge. For individual cell sorting, the signal processor is in normal inopertive condition to prevent sorting of drops from the drop stream. During this time all drops contained in the stream are caught by a stream catcher, and none are allowed to enter a tray well. When armed, by manual actuation of an arming switch, the circuit is conditioned to sort a single particle from the drop stream, at which time the circuit returns to normal inoperative condition. A tray support is provided for movable support of the multiwell tray along perpendicular X and Y directions, and a releasable detent releasably lock the tray support at any desired X-Y position. The tray support is provided with a target for use in initial alignment of the tray support relative to drops separated from the stream to assure entry of such drops into a tray well during subsequent operation of the cell sorter.

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San Francisco, CA, United States of America

David R Parks