Software and code


CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. More information can be found in the CellProfiler Wiki.

Download CellProfiler.

CellProfiler Analyst

CellProfiler Analyst allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complex and subtle phenotypes, for automatic scoring of millions of cells.

Download CellProfiler Analyst.


DeepProfiler is a set of tools that allow you to use deep learning for analyzing imaging data in high-throughput biological experiments. Please, see our Wiki documentation page for more details about how to use it.

Instructions to download DeepProfiler can be found on the Github page.


A web-based deep learning tool for classification of human cells, created with Tensorflow.js and React.