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

nnInteractive is a framework for 3D interactive segmentation, supporting intuitive prompts like points, scribbles, bounding boxes, and lasso. Trained on 120+ diverse 3D datasets, it sets a new stan…

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

R package to find the closest DMC floss to colours.

A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA sequencing

VIPER is a user-friendly software for assembling and identifying viral genomes (currently SARS-CoV-2, Dengue, and Influenza), from Illumina sequencing data generated through genomic surveillance.

Unified knowledge-driven network inference from omics data

A scanpy extension to analyse single-cell TCR and BCR data.

Accompanying code for Image2Omics

Example genomics data for tool developers

Interactive image stack viewing in jupyter notebooks based on ipycanvas and ipywidgets

A sandbox for benchmarking detection of out-of-reference cells in single-cell genomics data

Single-cell perturbation analysis

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

most pretty & lovely tables with matplotlib

Deep-neural protein translation

Reference mapping for single-cell genomics

Single-cell spatial elucidation through image-augmented graph transformer

We will upload here the material and the code of the napari workshop held in Milano on Sept 26-27th 2023

A fancy and practical functional tools

Static plotting for spatialdata

A tool for semi-automatic cell type classification

Conversion between scRNA-seq objects

A tool for refurbishing and modernizing Python codebases

🚀 A simple way to train and use PyTorch models with multi-GPU, TPU, mixed-precision

Tracking and collecting papers/projects/others related to Segment Anything.

This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging.

An analysis pipeline in CellProfiler and R for analysis of Whole-slide immunofluorescence image data

Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics