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_im2imA generic toolbox for microscopy image to image transformation
SOFTWARE - EfficientBioAIA toolbox for bioimaging model compression
Open datasets
Other open science works from our group members
SOFTWARE - 3D cell cycle classifiermitotic classifier
SOFTWARE - Iterative ML segmentation for 3D microscopy imagesThis is the ML part of Allen Cell and Structure Segmenter software
SOFTWARE - Classic image segmentation for 3D microscopy imagesThis is the classic part of Allen Cell and Structure Segmenter software
Data - 3D single cell dataset with cell stage annotationDataset used to train the 3D mitotic classification
Other open source tools from the community (we would highly recommend)
ZeroCostDL4MicA 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.
napariA fast, interactive, multi-dimensional image viewer for Python, designed for browsing, annotating, and analyzing large multi-dimensional images
BioImage Model ZooA 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.