Microscopy Machine Vision Lab

Open Science Portal

Our group is fully commited to open science, from developing/contributing to open source softwares to building public datasets for AI research as well as open access publications. We believe open science can lead to impactful big science. Currently, our group has a special focus on building AI-based biomedical image analysis methods/tools/datasets for light-sheet fluorescence microscopy (LSFM) imaging. Meanwhile, on this page, you can also find other open science works our group members built before, other than LSFM, as well as a curated list of open science tools developed by other researchers in the community that we would highly recommend.

Open source softwares

SOFTWARE - mmv_im2im

A generic toolbox for microscopy image to image transformation

SOFTWARE - EfficientBioAI

A toolbox for bioimaging model compression

Open datasets

Other open science works from our group members

SOFTWARE - 3D cell cycle classifier

mitotic classifier

SOFTWARE - Iterative ML segmentation for 3D microscopy images

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

SOFTWARE - Classic image segmentation for 3D microscopy images

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

Data - 3D single cell dataset with cell stage annotation

Dataset used to train the 3D mitotic classification

Other open source tools from the community (we would highly recommend)


A collection of self-explanatory Jupyter Notebooks for Google Colab that features an easy-to-use graphical user interface. A good resource for learning deep learning applications in microscopy image analysis.


A fast, interactive, multi-dimensional image viewer for Python, designed for browsing, annotating, and analyzing large multi-dimensional images

BioImage Model Zoo

A community-driven AI model repository designed to promote the adoption of AI methods within the bioimaging community. Its objective is to provide a diverse and user-friendly collection of pretrained models dedicated to bioimage analysis tasks.