Image Analysis

Visualize and Quantify Image Data

We provide four high-end workstations and support several image analysis packages for visualization, quantification and restoration of light microscopy, or LM, image data. We offer tailored consultation on the analysis of electron microscopy, or EM, images. And, we can advise and train you to conduct quantitative data analysis on your own.

Thanks to our joint arrangement with the Genomics & Bioinformatics shared resource, services are available to assist you with quantifying your imaging data in a rigorous and meaningful way.

Schedule With Us

To learn more about image analysis services or to schedule a consultation, please contact:

Julien Dubrulle, Ph.D.
Morphometric and Image Analysis Scientist

Location: Arnold Building M1-A101; Thomas Building DE-512

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Imaging workstations, software and features

Imaging workstations:

  • Windows 10, 64-bit, Intel Xeon W-2295 3.0GHz 18 core, 512GB RAM, NVIDIA Quadro RTX 6000 24GB
  • Windows 10, 64-bit, AMD Ryzen Threadripper 3990X 2.9GHz 64 core, 256GB, 2x GeForce RTX 2080 TI 11GB
  • Windows 10, 64-bit, Intel i9 7900X / 3.30 GHz, 128 GB RAM, multiple data drives for storage
  • Windows 7 SP1, 64 bit, Intel Xeon / 2.67 GHz, 48GB RAM, multiple data drives for storage

Supported software:

  • Imaris 
  • Volocity 
  • AutoQuant 
  • TissueQuest and HistoQuest
  • Nikon NIS Elements
  • ImageQuant TL
  • Li-Cor Image Studio
  • Adobe Photoshop
  • ImageJ/FIJI
  • Leica LAS X
  • Zeiss ZEN
  • Cell Profiler
  • MATLAB

Highlighted features: 

  • 3D reconstructions
  • Quantify fluorescent intensities, shapes and volumes
  • Deconvolve epi-fluorescent image data sets
  • Track dynamics of moving objects
  • Study interactions of multiple populations
  • Convert 3D time-lapse data into movies
  • Single particle analysis
Image analysis image
Image by Andrea Doak, Cheung Lab, Fred Hutch
Morphometrics and image analysis

We can perform analysis on virtually any input, including:

  • Datasets: 2D, 3D, time-lapse, multi-well/high-throughput
  • Image formats, both nonproprietary (e.g., .tif, .jpg, png) and commonly used biomedical formats (e.g., .dv, .lsm, .czi, .nd2)
  • Samples: cultured cells, tissue sections, organoids, embryos, small organisms
  • Labeling, including label-free (phase contrast, brightfield), fluorescence (IF, FISH, fluorescent proteins/dyes) and histochemistry (IHC, H&E, cell-type specific stains)

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

  • Cell/spot/object counting
  • Subcellular localization, including location of subcellular structures and organelles, nucleocytopasmic ratio, and density of objects of interest in a cellular compartment
  • Signal colocalization
  • Morphometric analysis, including surface, volume, circularity, eccentricity, solidity and texture
  • Spatial distribution, including position of cells, crowding or neighbor occupancy
  • Cell tracking, including position, path and time-related metrics
  • Wound healing assays
  • High-throughput screening
Tracks
Single cell tracks. Each cell track is depicted in a different color with the starting point defined by a black dot. Data from the Hatch Lab, Fred Hutch
Dynamics of wound healing in a Drosophila syncytial embryo. Left panel: Time-lapse movie of wound-induced epithelial layer of an embryo labeled with fluorescent actin protein. Right panel: Processed data showing the hole extent in green and the actin ring in magenta. Video by M. Nakamura, Parkhurst Lab, Fred Hutch

Questions about our image analysis services or how to schedule with us?