Stars
This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of top…
Arch Linux Niri configuration for photography, gaming, and content creation. Features gradient borders, J.A.R.V.I.S. integration, audio routing, and comprehensive documentation.
Package for the analysis of Transcripts outside segmented cells in ST data
Variational inference for exponential family distributions as linear regression, in JAX.
Multipurpose Gaussian Process library
An extensible, state-of-the-art framework for columnar compression, and the fastest FOSS columnar file format. Formerly at @spiraldb, now an Incubation Stage project at LFAI&Data, part of the Linux…
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
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
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
Poisson-randomized gamma Poisson matrix factorization
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.