Morphometry and Image Analysis

Contact: Julien Dubrulle, PhD
Location: Arnold M1-A101 | Thomas DE 512
Contact phone: (206) 667-6391
Contact e-mail: jdubrull@fredhutch.org

The joint arrangement between the Bioinformatics and Cellular Imaging Shared Resources provides services to assist researchers with quantifying their imaging data in a rigorous and meaningful way. Analysis can be performed on virtually any input, including:

3D reconstruction of a patient-derived high-grade glioma tumor cell labelled with FGFRI receptor (green) and the Golgi protein GM130 (red). Credits: Dayoung Kim, Cooper Lab

DATASETS: 2D, 3D, time-lapse, 4D, multi-wells/high-throughput

IMAGE FORMATS: non-proprietary (e.g., .tif, .jpg, .png), and commonly used bio-formats (e.g., .dv, .lsm, .czi, .nd2)

SAMPLES: cultured cells, tissue sections, organoids, embryos, small organisms

LABELLING: Label-free (phase contrast, brightfield), fluorescence (IF, FISH, fluorescent proteins/dyes), histochemistry (IHC, H&E, cell-type specific stains)

We apply custom-made, versatile image analysis pipelines to extract quantitative metrics related to:

Nuclear segmentation of U2OS cells expressing a nuclear-localized GFP. Red crosses indicate the position of the centroid of each nucleus, and red lines delineate the perimeter of each nucleus. Credits: Lucian DiPeso, Hatch Lab

Cell/Spot/Object Counting: Determine total number of cells/objects or fraction of positive/negative cells/objects for different markers.

Subcellular Localization: Determine localization of signal within the cell (e.g., nucleus, cytoplasm, membrane, organelles). Extract nucleocytoplasmic ratio for transcription factors and shuttling proteins. Determine density/number of objects of interest (speckles, stress granules, organelles, bacteria, single molecules from FISH) in a given cellular compartment.

Signal Colocalization: Determine the extent of colocalization between different signals using Mander’s coefficients or Pearson’s analysis.

Morphometric Analysis: Determine shape-related metrics of objects, such as surface, volume, circularity, eccentricity, solidity, texture.

Spatial Distribution: Determine absolute and relative position of cells, crowding or neighbor occupancy.

Cell Tracking: Determine position, path and time-related metrics of cells/objects from time-series image datasets.

Wound Healing Assay: Determine rate of gap closure in classic wound healing experiments.

High-Throughput Screening: Analyze image-based chemical/biochemical medium/high-throughput screens. Perform QC and hit selection based on biological questions and available markers.

We also provide consultations and guidance before, during and after projects to ensure the best possible outcome in terms of grants, publications and personal accomplishment.