Quantitative Image Analysis and Visualization

Location: Thomas Building, DE-512
Contact phone: (206) 667-4205
Contact e-mail: imaging@fredhutch.org

Quantitative image analysis (image cytometry) encompasses a range of techniques for extracting objective, quantitative information from microscopy images. While flow cytometry is a proven technique to analyze cell populations by providing cell size and fluorescence intensity for multiple markers, image cytometry can provide similar information for adherent cells or tissue sections, as well as a wealth of additional information such as cell shape and size, intracellular localization of fluorescence intensity for multiple markers, counting of cells or intra-cellular organelles, and more. The resource provides training and assistance with a variety of image cytometry techniques including:

  • Cytometric analysis of cells in micro-plate format (high content analysis) with the Thermo/Cellomics Arrayscan platform and high content informatics analysis package
  • Cytometric analysis of slides, including cell smears, tissue sections, and tissue micro-array (TMA) slides. Our analysis software is compatible with immunofluorescent staining (TissueQuest), as well as immunohistochemical staining (HistoQuest software).
  • Whole well imaging (Cellomics and Incucyte platforms)
  • Validated end point and kinetic assays: cell proliferation, cell invasion, cell morphology, reporter gene expression, live/dead assays, and more (Incucyte and Cellomics platform).
  • 3-D measurements: Volume and intensity measurements, including co-localization, for 3-D data from deconvolution or confocal microscopes.
  • Custom analysis: we will try to develop an analysis protocol for your specific needs.

The resource also provides access to the high end 3-D image visualization and measurement software Volocity and Imaris, along with training and support. Volocity and Imaris accept multi-dimensional microscopy data files from most of our microscope systems, and allow researchers to visualize multi-dimensional data (3-D image stacks in multiple channels over time).

3-D renderings of microscopy data can be saved as movies for publications and presentations. These software also provide powerful tools to extract quantitative information from 3-D data sets (such as counting particles, measuring volumes and intensities, and measuring colocalization of multiple markers).

Instrumentation: Thermofisher/Cellomics Arrayscan VTi, Essen Biosciences Incucyte, Tissuegnostics Tissuefax system.

Software: Cellomics High content informatics, Incucyte analysis software, TissueQuest, HistoQuest, StrataQuest, Metamorph, ImageJ, Imaris, Volocity.

Scheduling time for instruments, training, and support:

To schedule time on any of our microscopes, or to schedule staff assistance or training, please use iLab. The resource is open to all from 9:00 AM - 5:00 PM, Monday through Friday. After hours access can be granted to experienced users and requires training by the resource's staff. Please contact Scientific Imaging for further details.

How to access your data:

Data acquired on Scientific Imaging instruments is transferred to the si folder in the user's fred account. If you do not have a fred account, please submit the computing account application form. Once you have obtained a fred account, please contact Scientific Imaging so that we can create an si link for you. External users without access to fred can obtain their data via ftp, or can download to their own data storage device from one of our dedicated computers. Please note that no portable drives are allowed on instrument computers.