Light Microscopy Services

Light Microscopy

Our light microscopy, or LM, facility offers investigators an extensive set of microscopy services equipment for LM imaging and analysis and world-class expertise. Our experienced team offers investigators consultation, training and services in all LM modalities.


Services  |  Image Analysis  |  Microscopes

Schedule With Us

To schedule LM services with the Cellular Imaging shared resource, or to get more information about how we can work with you, contact our director.

Dr. Peng Guo
Cellular Imaging core director


Fluorescence microscopy and brightfield microscopy

We have an extensive set of microscopy instruments including widefield microscopes, incubator microscopes, a digital slide scanner, a high-content reader, a confocal microscope, a super-resolution microscope and light sheet technologies.

Our team can provide you with consultation, training, development or assisted sessions.

Fluorescence microscopy and brightfield microscopy image
Image by Cellular Imaging core staff
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Quantitative gel and blot imaging and analysis

We operate two scanners and dedicated software for the imaging and quantitative analysis of gels, blots and plates, including applications such as Northern, Southern and Western blots, In-Cell Westerns and more.

Our team provides training for all first-time users. Upon request, our team can scan and analyze your blots.


Quantitative gel and blot imaging and analysis image
Image by Cellular Imaging core staff

Karyotyping human and mouse cell lines

Karyotyping is the analysis of chromosomes in a cell. A karyotype determines the number and appearance of chromosomes and detects chromosomal abnormalities such as missing or extra chromosomes (aneuploidies), as well as a variety of chromosomal aberrations (such as deletions and translocations). We offer a limited karyotyping service for research only — for example, to test cell lines. We karyotype human and mouse cells and may consider other species.

Karyotyping human and mouse cell lines image
Image by Cellular Imaging core staff

Image Analysis

We provide four high-end workstations and support several image analysis packages for visualization, quantification and restoration of LM image data. We also can advise and train you to conduct quantitative data analysis on your own.

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

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

Customized image analysis in MATLAB

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.

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
MATLAB contact information

Julien Dubrulle, Ph.D.
Phone: 206.667.6391
Location: Arnold Building M1-A101; Thomas Building DE-512

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


Widefield microscopy

Nikon Eclipse E800 is an upright fixed-stage microscope, suitable for collecting 2D images (no stacks) in transmitted light and/or fluorescence mode.

DeltaVision is a versatile widefield imaging microscope with 3D deconvolution functionality.

Nikon Live is a widefield fluorescence microscope system as well as a transmitted light imaging system in DIC and phase contrast modes. The microscope is primarily used for time-lapse imaging of living samples.

Nikon TIRF/STORM is a widefield fluorescence and total internal reflection fluorescence, or TIRF, microscope with super resolution (also called N-STORM). 

Widefield microscopy image
Image by Elizabeth Steenkiste, Cooper Lab, Fred Hutch

Incubator microscopy

Incucyte (S3 and Zoom) is an incubator microscope system for long-term, live-cell imaging.

Incubator microscopy
Image by Cellular Imaging core staff

Digital slide scanner

Our TissueFAXS system is an automated digital pathology system/slide scanner for the imaging of histology slides and multi-fluorescently labeled slides, including large tissue sections and tissue microarray slides.

Digital slide scanner image
Image by Kimberly Smythe, Pollack Lab, Fred Hutch

High-content reader

Our Molecular Devices ImageXpress is a dedicated microscope with confocal ability for the automated imaging and analysis of samples in multi-well plate format, and it is specifically designed for high-content analysis and for image-based screening applications.

High-content reader image
Image by Jessica Wagoner, Polyak Lab, University of Washington

Confocal microscopy

Our Leica SP8 is a versatile confocal imaging platform with stimulated emission depletion, or STED, super-resolution capability.

Our Zeiss 780 is a confocal microscope with super-resolution capability and multi-photon excitation.

Light sheet microscopy

Our LaVision Ultramicroscope II light sheet system is used for 3D imaging and analysis of entire biological systems using a “sheet” of laser illumination.

Light sheet microscopy image
Image by Wiley Analytical Science

Gel and blot imaging

We operate two scanners and dedicated software for the imaging and quantitative analysis of gels, blots and plates, including applications such as Northern, Southern and Western blots, In-Cell Westerns and more.

Our team provides training for all first-time users. Upon request, our team can scan and analyze your blots.

Our GE Typhoon Trio is a multimode scientific scanner for fluorescence, chemiluminescence and radioactivity detection (phosphorimager) using visible lasers.

Our Li-cor Odyssey near-infrared scanner is a scientific fluorescent scanner for gel, blot, plate and slide imaging using infrared lasers.

Questions about our LM services or how to schedule with us?