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OSSI-supported Projects

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OSSI-supported Projects
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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.)

Maintain, extend, adapt and document Suite2p and Cellpose.
[YouTube link] [GitHub Cellpose] [GitHub Suite2p] [Project Description]

BigWarp (Bogovic & Saalfeld)

Maintain and extend BigWarp (3D non-rigid registration for very large volumes).
[YouTube link] [GitHub] [Project Description]

Kilosort (Pachitariu et al.)

Maintain and develop python version of Kilosort (electrophysiology data).
[YouTube link] [GitHub] [Project Description]

Video annotation software (Branson et al.)

Develop a usable and extensible library for video annotation for machine learning.
[YouTube link] [GitHub coming soon ...] [Project Description]

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.)

[YouTube link] [GitHub BigStitcher] [GitHub Stitching-Spark] [Project Description]

Spatial Transcriptomics Tools (Preibisch et al.)

Maintain and extend RS-FISH (smFISH spot localization) and STIM (handling spatial transcriptomics data).
[GitHub RS-FISH] [GitHub STIM] [Project Description]

An open-source platform for single-molecule localization
(Turaga et al.)

Develop a user-friendly (napari) deep learning-based single-molecule detection software.
[GitHub] [Project Description]

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.)

Maintain and extend Paintera (3D annotation software for very large volumes).
[GitHub] [Project Description]

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.)

Develop documentation for the interactive VVD 3D viewer/renderer for very large image volumes.
[GitHub] [Project Description]

Cell Videos from High-Level Descriptions (Hubbard)

Make the neuVid 3D visualization software more accessible to the community.