Cell Profiler

CellProfiler is a free, open-source software developed by the Carpenter lab which is designed to analyse cellular images in batch. Where other softwares can be automated to apply processes in batch, CellProfiler is set up to do this automatically. It specialises in 2D segmentation and analysis of objects (e.g. cells and nuclei) within images but can also be used for 3D and tracking.

Facility Resources
  • A general guide to using CellProfiler as well as more specific protocols that we thought would be helpful for users can be found here or as videos here.
  • CellProfiler works based on pipelines. The facility has produced some pipelines that be Github along with a short guide of how to utilise them.
  • More general information on image analysis concepts and terms can be found here.
  • If you would like to know if there is a relevant workshop coming up soon please check here.

External resources

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