napari: a fast, interactive, multi-dimensional image viewer for python

A minimal Zarr image viewer based on Viv.

Spatial cellular architecture predicts prognosis in glioblastoma - Nature Communications

HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024 (Spotlight)

Python library to handle Gene Ontology (GO) terms

A scikit-learn compatible neural network library that wraps PyTorch

Data and code for Emotion Prediction Errors

A repository for Nature Communications paper

Language sentiment data and analysis scripts for "Language sentiment predicts changes in depressive symptoms"

Definitions for a collaborative cryoET annotation tool.

A reactive notebook for Python — run reproducible experiments, execute as a script, deploy as an app, and version with git.

Parallel computing with task scheduling

Advanced Normalization Tools (ANTs)

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

Download data from private S3 buckets into Google Sheets. Function to create GET signed URLs for AWS S3.

This repository contains the python package for Helical

End-to-end light-sheet image analysis for mouse brains, with DL training data generated in VR

Segment Anything in Medical Images

PyTorch3D is FAIR's library of reusable components for deep learning with 3D data

Code associated to the publication: Scaling self-supervised learning for histopathology with masked image modeling, A. Filiot et al., MedRxiv (2023). We publicly release Phikon 🚀

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

Nonnegative spatial factorization for multivariate count data

FalseColor Python is a rapid digital staining module designed for translating two-channel fluorescence images (i.e. a nuclear and cytoplasmic stain) to the traditional H&E histopathology color space.

the Vascular Modeling Toolkit

Distributed image processing

🎓 Path to a free self-taught education in Computer Science!

StarDist - Object Detection with Star-convex Shapes

Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.