Center for Open Bioimage Analysis
Published February 22, 2023 | Version v2
Peer review Open

Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization

Creators

  • 1. Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, Brazil and Broad Institute of MIT and Harvard, Cambridge MA USA 02142
  • 2. Broad Institute of MIT and Harvard, Cambridge MA USA 02142
  • 3. Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, Brazil

Description

Image-based profiling quantitatively assesses the effects of perturbations on cells by capturing a breadth of changes
via microscopy. Here we provide two complementary protocols to help explore and interpret data from image-based
profiling experiments. In the first protocol, we examine the similarity among perturbed cell samples using data from
compounds that cluster by their mechanism of action (MOAs). The protocol includes steps to examine feature-driving
differences between samples and how to visualize correlations between features and treatments to create interpretable
heatmaps using an open-source web tool, Morpheus. In the second protocol, we show how to interactively explore
images together with the numerical data, while we provide scripts to create visualizations of representative single cells
and image sites to understand how changes in features are reflected in the images. Together, these two tutorials help
biologists and researchers interpret their image-based data to speed up research.

Notes

Data are available at https://github.com/ciminilab/2022_Garcia-Fossa_submitted. Funding was provided by the National Institutes of Health (NIH COBA P41 GM135019 to BAC and AEC and MIRA R35 GM122547 to AEC). This project has been made possible partly by grant number 2020-225720 to BAC from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation. São Paulo Research Foundation (FAPESP) was also provided funding #2022/01483-4, #2019/24033-1, and #2020/01218-3. SS and AEC serve as scientific advisors for companies that use image-based profiling and Cell Painting (AEC: Recursion, SS: Waypoint Bio, Dewpoint Therapeutics) and receive honoraria for occasional talks at pharmaceutical and biotechnology companies.

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Additional details

Related works

Is published in
Journal article: 10.1002/cpz1.713 (DOI)

Funding

National Institutes of Health
Extracting rich information from biological images 5R35GM122547-02