Below you will find a list of OSSI-supported projects. We are in the process of uploading presentations for each project, which are published in the YouTube OSSI Playlist. Links to individual projects and GitHub pages can be found below.
Cellpose and Suite2p (Stringer et al.)
BigWarp (Bogovic & Saalfeld)
Kilosort (Pachitariu et al.)
Video annotation software (Branson et al.)
Peta-scale lightsheet processing (Preibisch & Saalfeld)
Developer-friendly & user-friendly software for processing peta-byte scale lightsheet datasets.
Merged with the following proposal:
- Maintain and extend EASI-FISH software (Wang et al.)
[GitHub] [Project Description]
- Image Processing Pipelines for Lightsheet Data Reconstruction (Desantis et al.)
Spatial Transcriptomics Tools (Preibisch et al.)
An open-source platform for single-molecule localization
(Turaga et al.)
Janelia Horta Cloud (Rokicki et al.)
HortaCloud is a cloud-based collaborative annotation system for terabyte-scale sparse volume annotation. This platform was developed by Scientific Computing for the MouseLight Team Project and has allowed annotators to efficiently reconstruct entire axonal arbors of over 1000 individual neurons from whole-brain light microscopy data.
[YouTube link] [GitHub]
Paintera (Saalfeld et al.)
Java packaging tool chain (Saalfeld et al.)
Develop an easy-to-use packaging system for Java applications.
[GitHub coming soon ...] [Project Description]
VVD Viewer (Kawase et al.)
Cell Videos from High-Level Descriptions (Hubbard)
Make the neuVid 3D visualization software more accessible to the community.