Colony formation assays (also called clonogenic assays) are the method of choice to asses the in vitro self-renewal capacity of cells since more than 50 years. The method is easy to perform, low-cost, and generates reliable results about efficacy of therapeutic interventions (irradiation, chemotherapeutic drugs, etc.).

Due to technological limitations, most researchers have limited their analysis to either the total number of colonies or the area covered by colonies. However, one look under a microscope reveals a striking variety in the morphology of the colonies. This variety has been directly linked to the self-renewal and tumor-initiating capacity of the colonies (see the literature section).

Most commonly three kinds of colonies can be identified:

  • Paraclones (small irregular colonies containing mostly differentiated cells)
  • Holoclones (densely packed colonies with a smooth and regular outline containing small individual cells)
  • Meroclones (intermediate between Para- and Holoclones, containing a mixed population of cells).

So far, identification of the colony type was only possible by manual inspection and identification of each colony under a microscope. This time consuming procedure is very prone to experimental and inter-observer bias leading to a low reproducibility of the results. However, advances in machine learning have dramatically increased the capabilities of computers to analyze images. The CATCH-colonies software integrates sophisticated analysis algorithms to analyze scans from a standard office scanner to provide a fast and unbiased analysis of the colony morphology. Simply download the software and analyze your experiments.