Open source code for AlphaFold 2.

Image processing in Python

LPIPS metric. pip install lpips

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

Morphological snakes for image segmentation and tracking

An open and interoperable data framework for spatial omics data

Code for ColabDock paper

Toolbox for the analysis of smFISH images.

Utils and convenience functions for large-scale bio-image analysis.

a minimal, scriptable genome browser for python

Analyzing cellular niches in spatial transcriptomics data

A tiny Python library for writing multi-channel TIFF stacks.

Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.

Feature extraction from GEOJson nuclei and tissue segmentation maps

A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.

tools for finding discrete bright spots in images (for multiplexed FISH, includes background subtraction, deconv, and blob detection)