Stars
A napari plugin for making animations
napari: a fast, interactive, multi-dimensional image viewer for python
Spatial cellular architecture predicts prognosis in glioblastoma - Nature Communications
Integrating histology and spatial transcriptomics - NeurIPS 2024
Python library to handle Gene Ontology (GO) terms
A scikit-learn compatible neural network library that wraps PyTorch
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, query with SQL, execute as a script, deploy as an app, and version with git. All in a modern, AI-native editor.
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.
A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.
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.
🎓 Path to a free self-taught education in Computer Science!
StarDist - Object Detection with Star-convex Shapes