DeepProfiler

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.

Cytominer

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

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).
 

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. More information can be found on the Copairs GitHub page.

Starrynight

Starrynight is a Python package that provides a pipeline for processing pooled Cell Painting data and related utility functions. More information can be found on the Starrynight GitHub page.

Pipecraft

Pipecraft is a Python library for creating execution engine-agnostic data processing pipelines using a Pythonic approach. More information can be found on the Pipecraft GitHub page.

Cytoskel 

Cytoskel is a Python library and set of tools for managing Infrastructure as Code (IaC) for the Imaging Platform. More information can be found on the Cytoskel GitHub page.

JUMP Babel

JUMP Babel is a Python tool that translates gene names between various identifiers, including Broad IDs, JUMP IDs, and NCBI identifiers. More information can be found on the JUMP Babel GitHub page.

JUMP Portrait

JUMP Portrait is a Python package that fetches JUMP images from CellPainting's AWS servers and provides utilities for exploring file names. More information can be found on the JUMP Portrait GitHub page.

CPG Tools

CPG Tools is a collection of Python packages that enhance the accessibility and data quality of the Cell Painting Gallery:

cpgdata

cpgdata provides data access and management functions for the Cell Painting Gallery. More information can be found on the cpgdata GitHub page.

cpgparser

cpgparser offers parsing utilities for Cell Painting Gallery data. More information can be found on the cpgparser GitHub page