A Python toolkit for quantitative and visual quality control of segmentation and transcript assignment in spatial omics data.

Simple color conversion and perceptual (DeltaE CIE 2000) difference

The best ChatGPT that $100 can buy.

Lower-latency OpenMP-style minimalistic scoped thread-pool designed for 'Fork-Join' parallelism in Rust and C++, avoiding memory allocations, mutexes, CAS-primitives, and false-sharing on the hot p…

Biomni: a general-purpose biomedical AI agent

Genome browser and variant annotation

A set of jupyter notebooks for the practice of TDA with the python Gudhi library together with popular machine learning and data sciences libraries.

Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.

Generate a spatial catalogue from multiplexed imaging data

Join subcellular Visium HD bins into cells

Poisson-randomized gamma Poisson matrix factorization

Simulate biological cells

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

Code to reproduce analysis from Cook et al., bioRxiv, 2023

Spectral unmixing of highly mixed multispectral flow and image cytometry data.

Voronoi tesselations in Julia

Latent Embedding Multivariate Regression

Sub-cellular spatial transcriptomics Cell Segmentation

A hybrid sampler for the Pólya-Gamma distribution in Julia, implementing multiple algorithms for efficient sampling.

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

A markup-based typesetting system that is powerful and easy to learn.

Code used to benchmark Xenium

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

The entmax mapping in JAX