Software and code


deepprofiler logo DeepProfiler is a set of tools that allow you to use deep learning for analyzing imaging data in high-throughput biological experiments. 

Documentation and instructions for DeepProfiler can be found in our Handbook and the code is located on the GitHub page.



The Pycytominer Python package is a suite of common functions used to process high dimensional readouts from high-throughput single cell experiments. More information can be found on the Github page.

CellProfiler and CellProfiler Analyst

CellProfiler logo Our lab previously launched and led the CellProfiler and CellProfiler Analyst projects, beloved by biologists around the world for bioimage analysis and cited over 15,000 times. They are now developed and maintained by the Cimini lab (since 2021).