Cell Biology

CellposePython

A generalist algorithm for cellular segmentation with human-in-the-loop training and superhuman generalization across diverse microscopy images.

DeepCellPython

A deep learning library for single-cell analysis of biological images, specializing in cell segmentation and tracking.

UsiigaciJupyter Notebook

A semi-automated pipeline for instance-aware cell segmentation, tracking, and migration analysis in phase contrast microscopy using Mask R-CNN.

CellProfiler AnalystPython

Interactive exploration and analysis software for large, high-dimensional image-derived biological data with supervised machine learning.

scPRINTJupyter Notebook

A large transformer foundation model for single-cell RNA sequencing data analysis, including gene network inference, denoising, and cell annotation.