A citation will be added here once the paper is published.
Suite3D is free software, released under the AGPL-3.0-or-later licence. The source, the demo notebooks and the analysis in this site are all in one repository:
https://github.com/alihaydaroglu/suite3d
pip install git+https://github.com/alihaydaroglu/suite3d.gitSee the quickstart for the GPU requirements and for running a demo end to end.
The three example recordings used by the demos are
deposited on figshare. The demos do not download anything: unpack the archive and point
--data-root at the folder.
https://rdr.ucl.ac.uk/articles/dataset/Volumetric_2-photon_imaging_datasets_used_to_test_Suite3D/32956220
DOI: 10.5522/04/32956220.v1
| Dataset | --data-root folder | Download | |
|---|---|---|---|
| V1 | v1/raw/*.tif |
21.1 GB | Mouse V1, 7 planes, standard resonant two-photon |
| LBM | lbm/raw/*.tif |
56.2 GB | Light-bead microscopy, 22 planes |
| Hippocampus | hippocampus/raw/*.tif |
21.1 GB | Dense, low-contrast, 4 planes |
Every result on this site — the processing-steps panels, the ROI traces and the 3D viewers — is produced from these recordings by the pipeline in the repository above, at the parameters recorded in each demo's notebook.