Open Science Portal

We are fully committed to open science: open-source software, public datasets and benchmarks built for AI research, and open-access publications. Open science makes impactful science. Below you find the tools and data released with our papers and earlier open-science work by our group members.

Software 25 Datasets 8 Earlier work 3

Open-source software

mmv_im2im

toolbox for microscopy image to image transformation

Code

EfficientBioAI

A toolbox for bioimaging model compression

Code

Leonardo

A toolbox for LSFM destriping and fusion

Code

mmv_h4tracks

napari plugin for human-in-the-loop cell tracking and analysis

Code

VesselExpress

A toolbox for rapid vasculature analysis in 3D LSFM

Code

Agentic-J arXiv 2026

AI agent for ImageJ/Fiji that turns natural-language requests into documented, reproducible analysis scripts

Code

Orochi NeurIPS 2025

Versatile foundation model for biomedical image processing

Code

BioFile Finder Nature Methods 2026

Web app to search, organize, aggregate and share image data via metadata (web app, our portal scripts)

Code

AutoQC npj Imaging 2025

Diffusion-model-based automatic quality control for high-throughput microscopy

Code

INIF Nature Computational Science 2025

Implicit neural image fields for microscopy image compression

Code

SGI CVPR 2026

Structured 2D Gaussians for efficient, compact representation of large images

Code

FlowRoI npj Imaging 2026

Optical-flow-based RoI extraction for compressing high-throughput immune cell videos

Code

Microscopy image compression benchmark Biological Imaging 2024

Deep-learning-based compression for microscopy images, with trained checkpoints

Code

Ceb IEEE TMI

Boundary-based cell instance segmentation

Code

cellmig PLOS Computational Biology 2026

R/Bioconductor package for uncertainty-aware Bayesian analysis of live cell migration (source)

Package

ComplexEye analysis Nature Communications 2023

Cell segmentation and tracking pipeline for the ComplexEye array microscope

Code

MSI-Explorer Analytical Chemistry 2025

napari-powered tool for mass spectrometry imaging data analysis

Code

INFL arXiv 2026

Implicit neural federated learning for privacy-preserved omics analysis (data)

Code

Masked Diffusion Model (MDM) arXiv 2023

Masked diffusion as a self-supervised representation learner for segmentation

Code

MRI anomaly detection (IQA) IEEE BIBM 2025

Rethinking brain MRI anomaly detection from an image quality assessment perspective

Code

Active learning pipeline BVM 2025

Data-centric active learning for biomedical image instance segmentation

Code

Segmentation data efficiency IEEE BIBM 2025

Code for studying redundancy and forgetting in biomedical segmentation with Cellpose

Code

Manual annotation risk ICCV Workshops 2023

Code for “On the risk of manual annotations in 3D confocal microscopy image segmentation”

Code

LightMyCells IEEE ISBI 2024

Our solution to the LightMyCells challenge for label-free organelle prediction

Code

NucMorph analysis Cell Systems 2025

Analysis code for nuclear growth trajectories in hiPS cell colonies

Code

Open datasets

Cell migration data portal

Cell migration data portal (ISAS)

Website

LSFM data portal

Lightsheet Fluorescence Microscopy (LSFM) data portal (ISAS)

Website

BIABench arXiv 2026

Benchmark of end-to-end bioimage analysis tasks for evaluating AI agents (code, project page)

Data

AutoQC-Bench npj Imaging 2025

About 8,000 brightfield neutrophil images labelled for quality issues (BioImage Archive)

Data

ComplexEye migration movies Nature Communications 2023

Raw time-lapse movies of immune cell migration from the ComplexEye array microscope

Data

Neutrophil tracking videos BioImage Archive

Brightfield neutrophil videos from ComplexEye, used for cell tracking and FlowRoI compression

Data

MedShapeNet Biomedical Engineering 2024

Large-scale collection of 3D medical shapes for computer vision (web interface and Python API)

Website

3D single-cell dataset with cell-stage annotation

Dataset used to train the 3D mitotic classification

Data

Earlier work by our group members

3D cell cycle classifier

mitotic classifier

Code

Iterative ML segmentation for 3D microscopy images

This is the ML part of Allen Cell and Structure Segmenter software

Code

Classic image segmentation for 3D microscopy images

This is the classic part of Allen Cell and Structure Segmenter software

Code