CellProfiler roadmap
David Stirling edited this page Feb 26, 2021
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56 revisions
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:
- 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.
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.
- Linux
- MacOS M1 source installation
- macOS and OS X
- Opening CellProfiler on Mac OS 10.15.7
- Ubuntu 20.04
- Ubuntu 18.04
- Ubuntu 16.04 LTS
- Windows
- Conda
- Arch Linux
- CellProfiler as a Python package
- Interfacing with other software
- OMERO: Accessing images from CellProfiler
- Getting started using CellProfiler from the command line
- Adapting CellProfiler to a LIMS environment
- s3
- Plugins
- RunImageJMacro
- Orientation to CellProfiler code
- Module structure and data storage retrieval
- Concurrency Model - Analysis Mode and ZMQ Interfaces
- Issues