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CSIF computing's bioimage analysis projects

One of the roles of the CSIF is to provide expertise in assembling individual methods into complete bioimage analysis/processing pipelines for specific projects using Python/SciPy.

For any question, please contact Cedric Espenel (


Nucleus segmentation and YAP intensity analysis

This code implements a quantitative image analysis pipeline for the segmentation of nucleus and cytoplasm of hESCs in various conditions. These reconstructed cell volumes can be used to measure fluorescence intensity in other channels in the confocal images.

Project supporting


  • Eva Huang
  • Alex Dunn's lab


Microarray analysis

The script indentifies every well in the microarray and quantify the fluorescence intensity for every channel. It also allows to dynamicaly interact with the result of the quantification.

Project supporting


  • Vincent Dufour-Decieux
  • Shan X. Wang's lab


Tracking of cell division and infection by Toxoplasma Gondii

This pipeline allows to distinguish uninfected host cells from host cells that were infected during the course of the experiment, track the host cells over time, and then monitor each cell for division.

Project supporting


  • Suchita Rastogi
  • John Boothroyd’s lab
  • Source code: In construction