CellProfiler roadmap - CellProfiler/CellProfiler GitHub Wiki

We released CellProfiler 4.0!

The changes in this overhaul 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:

Future Directions

• Expanded support for tissue sections and other large image types.
• Revise the input modules.
• Unify ExportToDatabase and ExportToSpreadsheet into a single, better export module.
• Continuing to add 3D support to various CellProfiler modules.
• Overhauling the internal analysis worker system.
• Replacement of Centrosome with scikit-image methods.
• Migrate from Bio-Formats towards imageio.
• Introduction and expansion of a stable API with the cellprofiler-core module.

Projects distinct from CellProfiler

We’re also working on new applications and libraries:

• Piximi, an image annotation and machine learning classification app.
• 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.