CellProfiler and CellProfiler Analyst

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).
 

DeepProfiler

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

PyCytominer

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Pycytominer is a Python package comprising a suite of common functions used to process high dimensional readouts from high-throughput single-cell experiments.

cp_measure 

cp_measure is a Python library that extracts CellProfiler's core measurement capabilities into a modular, API-first tool designed for programmatic feature extraction in image-based profiling workflows.

Cubic

cubic is a Python library that accelerates processing and analysis of multidimensional bioimages using GPU-enabled operations, offering substantial speedups through its device-agnostic API that wraps scipy/scikit-image and cupy/cuCIM. 

Copairs

Copairs is a Python package that identifies hits in large-scale perturbation screens and evaluates the similarity between perturbations using the mean average precision (mAP) metric.

JUMP Babel

JUMP Babel is a Python tool that translates gene names between various identifiers, including Broad IDs, JUMP IDs, and NCBI identifiers.

JUMP Portrait

JUMP Portrait is a Python package that fetches JUMP images from CellPainting's AWS servers and provides utilities for exploring file names.