CellProfiler roadmap

Anne Carpenter edited this page Oct 27, 2017 · 55 revisions

We released CellProfiler 3.0!

It may take us awhile to recover from this pretty substantial overhaul, whose glorious details are described in a blog post. Meanwhile, CellProfiler is cited in well over 5,000 scientific papers!

Here is a sampling of what might be up next:


  • Python 3 compatibility
  • Continuing to add 3D support to various CellProfiler modules
  • dynamically discover and load CellProfiler modules
  • multi-platform packages with Wheel

Paying down technical debt

  • upgrade wxPython to wxPython-Phoenix
  • replace cellprofiler.analysis and cellprofiler.analysis_worker with Celery
  • decouple cellprofiler.gui from cellprofiler
  • replace centrosome with scipy, skimage, and sklearn
  • replace Bio-Formats with imageio
  • use Sphinx for documentation

Projects distinct from CellProfiler

We’re also working on new applications and libraries:

  • Cytominer, an R package for mining perturbations.
  • Keras-ResNet, state-of-the-art convolutional feature extraction.
  • Keras-RCNN, state-of-the-art image segmentation and object detection models.
  • Skopy, a fast and simple alternative to CellProfiler.
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