CellProfiler Analyst

CellProfiler Analyst helps biologists explore measurements from image-based experiments and train machine learning classifiers to recognize cell phenotypes. It runs on your own machine and works with data imported from CellProfiler, with a focus on large, high-dimensional datasets from high-throughput experiments.

Its interactive visualizations link measurements to images, so you can inspect the cells behind patterns in the data. That connection matters when a numerical difference needs a visual check, or when the phenotype you're studying is difficult to distinguish through measurements alone.

The supervised machine learning system learns to recognize complex or subtle phenotypes from a training set, then automatically scores cells. This makes it relevant to experiments where manually reviewing each cell would be impractical. The classifier can score millions of cells.

CellProfiler Analyst combines visual data exploration and trainable classification in a tool designed for biologists. It's written in Python and distributed under a BSD license.