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Related Experiment Video

Updated: Apr 21, 2026

Clonogenic Assay: Adherent Cells
05:30

Clonogenic Assay: Adherent Cells

Published on: March 13, 2011

49.6K

Open access to high-content clonogenic analysis.

Fernanda Ricci1, Aishwarya Subramanian2, Mark Wade2

  • 1Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy fernanda.ricci@iit.it mark.wade@iit.it.

Journal of Biomolecular Screening
|November 9, 2014
PubMed
Summary
This summary is machine-generated.

The Colony Assay Toolbox (CAT) offers detailed single-colony analysis for clonogenic assays, extracting phenotypic data beyond simple counts. This user-friendly workflow enhances high-content screening capabilities for drug discovery.

Keywords:
CellProfilercolonieshigh contentp53wide-field microscope

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Area of Science:

  • Cell Biology
  • Bioinformatics
  • Drug Discovery

Background:

  • Current image analysis for clonogenic assays provides limited phenotypic data.
  • Existing methods lack user-friendly pipelines for high-content analysis of cell colonies.
  • Single-colony level phenotypic information is crucial for understanding cellular responses.

Purpose of the Study:

  • To introduce the Colony Assay Toolbox (CAT), a novel image analysis workflow for clonogenic assays.
  • To enable multiparametric, single-colony level phenotypic data extraction.
  • To provide a user-friendly pipeline for high-content analysis of cell growth and senescence.

Main Methods:

  • Developed an experimental and multiparametric image analysis workflow (CAT) for multiwell plate clonogenic assays.
  • Utilized open-source CellProfiler for colony image analysis with common wide-field fluorescent microscopes.
  • Employed a single fluorescent dye for all segmentation steps, ensuring accessibility.

Main Results:

  • CAT extracts detailed phenotypic information, including colony/nuclei number, size, and morphology.
  • The pipeline accurately discriminates between senescent and nonsenescent cells within colonies.
  • Demonstrated CAT's efficacy using Nutlin-3a and ABT-737 on human osteosarcoma cells.

Conclusions:

  • CAT provides a robust and accessible solution for detailed clonogenic assay analysis.
  • The toolbox facilitates deeper insights into cellular responses and drug effects at the single-colony level.
  • CAT enhances high-content screening by enabling comprehensive phenotypic characterization.