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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 (espenel@stanford.edu).

PORTFOLIO

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

Link

  • 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

Link

  • 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

Link

  • Suchita Rastogi
  • John Boothroyd’s lab

 

Neuronal Activity

The script correct for any drift during imaging, extract the fluorescence traces and measure and plot the synchronicity between the cells.

Project supporting

Link

  • Humsa Vankatesh
  • Michelle Monje's lab