TIPSv2 (CVPR'26) and TIPS (ICLR'25)

A database of opsin genotype-phenotype data and machine-learning models trained to predict opsin phenotypes.

python tools for BigDataViewer

PyTorch implementation of MAE https//arxiv.org/abs/2111.06377

AlphaLink: Integrating crosslinking MS data into OpenFold

DeepSHAP XAI integration with ColabFold for AlphaFold2 prediction interpretation

KaroSpace is a viewer for spatial omics data

TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer,…

Template repo to write new papers

mini cli search engine for your docs, knowledge bases, meeting notes, whatever. Tracking current sota approaches while being all local

A modern and customizable python UI-library based on Tkinter

Finite-Element Assisted Brain Assembly System for stitching & alignment of connectomics data

Tool for segmentation-based deformable registration

Public RFDiffusionAA repo

Foldseek enables fast and sensitive comparisons of large structure sets.

Context Parallelism Code for Boltz-2

Uses DAP (Distributed Axial Parallelism) to prevent OOM when running Boltz-2 protein structure inference. Optional FlexAttention for triangle attention.

Parameter Efficient Fine-Tuning of Segment Anything Model

Segment Anything for Microscopy

[TPAMI 2025] UniMatch V2: Pushing the Limit of Semi-Supervised Semantic Segmentation

An open-source, code-first Python toolkit for building, evaluating, and deploying sophisticated AI agents with flexibility and control.

Flood-Filling Networks for instance segmentation in 3d volumes.

Shallow2deep: Exploiting feature-based classifiers for domain adaptation in semantic segmentation

A CLI tool to run edge classifiers trained in ilastik's Multicut workflow on large volumes using elf's blockwise multicut

A Python-based tool for parallelized conversion of image datasets from various formats to OME-Zarr, with support for distributed processing and multi-dimensional concatenation.

PyTorch implementation of the U-Net for image semantic segmentation with high quality images