3D Quantitative Visualization of Fluorescently Labeled Cells

The visual analysis, assembly, and communication of molecule-scale events has benefited greatly from an explosion of available tools and data that has been provided and evolved by the structural biology community over the past 40 years. Compared to molecular visualization, however, the data, tools, and techniques available for cell-scale visualization remain in a relative infancy.

This workshop is intended for biologists who want to learn ways to access, view, and interrogate 3D fluorescence microscopy data. It will cover several of the specific protocols and tools used and developed at the Allen Institute for Cell Science. Many of the workshop sessions will be based on data that is publicly available on, and the methods can be applied to any 3D fluorescence microscopy data.

Join us for a hands-on workshop to learn about and experiment with tools for whole-cell quantitative visualization. Members of the Allen Institute for Cell Science team will teach you how to perform many of the 3D visualization, analysis, and online presentation techniques used at the institute for the quantitative visualization of fluorescently labeled cells. As a group, we will further discuss alternative tools and outstanding needs for future development that we share as a community.




Due to the hands-on nature of this workshop and focused, small group discussions, we will limit the number of participants to less than 30. We encourage trainees and bench scientists interested in 3D visual analysis to apply.  We are eager to host a diverse audience at this workshop and will be providing travel awards to a few attendees based on scientific area of interest and financial need.

This workshop will be held in conjunction with the 2019 BioImage Informatics conference, October 2-4, at the Allen Institute. Conference registration and abstract submission is separate from the workshop application.

Applications are now closed. If you have questions about the workshop, please contact

Workshop topics

  • How to define and describe the type(s) of whole cell data we produce and work with at the Allen Institute for Cell Science

  • How to look at 3D fluorescence microscopy data to observe interesting biology
    • We will download examples of this type of data from
    • We will use a variety of freely available tools to perform visual analyses
    • We will provide methods for converting most any common 3D fluorescence microscopy data to the OME-TIFF file format standard that we use at the Allen Institute for Cell Science
  • How to segment 3D fluorescence microscopy data
    • We will describe popular tools you can use to perform both simple and complex measurements
    • We will walk through an extensive tutorial to teach you how to use the Allen Cell Structure Segmenter
  • Ways to measure and quantify 3D fluorescence microscopy data
    • We will convert segmentations to measurements, e.g. volume, surface area, 3D localization tendencies, nearest neighbors, textures, patterns, relative intensities, etc.
    • We will describe methods for absolute quantification, e.g. estimated protein counts
  • Next-generation machine learning tools for the analysis of 3D fluorescence microscopy data

Later in the workshop, there will be a hands-on group experiment to apply the tools you learned at the workshop. We will also discuss shortcomings encountered, other tools available, and the needs we have as a community for future tool development.