Oregon Health & Science University

Ventana Medical Systems, Inc.

Tania Vu

Thomas Jacob

Brian Jay Druker

Michael S Barnes

Joe W Gray

Christophe Chefd'hotel

Thomas M Grogan

David Chafin

Benjamin C Stevens

Karl Eric Garsha

Kandavel Shanmugam

Esteban Roberts

Franklin Ventura

Damien Ramunno-Johnson

Brian R Long

Benjamin K Scholl

Methods, systems, and apparatuses for detecting and describing heterogeneity in a cell sample are disclosed herein. A plurality of fields of view (FOV) are generated for one or more areas of interest (AOI) within an image of the cell sample are generated. Hyperspectral or multispectral data from each FOV is organized into an image stack containing one or more z-layers, with each z-layer containing intensity data for a single marker at each pixel in the FOV. A cluster analysis is applied to the image stacks, wherein the clustering algorithm groups pixels having a similar ratio of detectable marker intensity across layers of the z-axis, thereby generating a plurality of clusters having similar expression patterns.

Methods, systems, and apparatuses for quantitative analysis of heterogeneous biomarker distribution

Embodiments herein provide methods, apparatuses, and systems for detecting, monitoring, measuring, and/or characterizing the activity of phosphoproteins such as tyrosine kinases (TKs) and downstream proteins in TK signal transduction pathways (e.g., TK pathway proteins). In various embodiments, the methods, apparatuses, and systems may use nanoparticles, such as quantum dots (QD), to detect and/or characterize the abnormally overactive TK signaling pathways that underlie tumorgenesis and tumor progression. In various embodiments, the QD-based methods, apparatuses, and systems may have a sufficiently high degree of sensitivity to enable the identification of new TK signaling pathway markers, for example for use in diagnosing, staging, monitoring, and/or prognosing cancers, or in evaluating the efficacy of cancer therapeutics.

Methods apparatuses and systems for detecting and quantifying phosphoproteins

Methods and systems for quantifying cellular activity using labeled probes, e.g., quantum dots, are disclosed. In one example approach, a method for quantifying cellular activity in a sample containing intact cells having labeled complexes comprises receiving images of the sample at a plurality of depths and detecting individual intact cells in the images of the sample at the plurality of depths. For each detected cell, discrete labels may be detected and localized in the cell at each depth, a total number of detected and localized labels may be calculated in the cell, and an activity level of the target molecule for the labeled probe in the cell determined.

Cellular activity quantification using labeled probes

An apparatus and method for counting nanoparticle probes is disclosed. In one embodiment, quantum dot-tagged proteins on optically transparent membranes or slides are counted. The transparent membranes or slides are loaded onto a stage (e.g., an X-Y stage or X-Y-Z stage), which can automatically reposition the transparent membrane or slides for image capture at varying locations. A microscope can be used for providing a light source to fluoresce the nanocrystals and for providing the magnification needed for image capture. Once one or more images are captured, the nanoparticles can be automatically counted using post-processing software that maintains a total count across multiple images, if desired.

Automated detection and counting of biomolecules using nanoparticle probes

Growing community of inventors

Portland, OR, United States of America

Tania Vu