CATAN
CATAN (Curation and Analysis of Tracked Across-sessions Neurons) is an open-source, cross-platform toolbox for the analysis, tracking and curation of neuronal populations in longitudinal calcium imaging experiments.
It provides an interactive GUI together with a Python API for
- visualization of calcium imaging sessions
- ROI inspection
- registration and remapping between sessions
- probabilistic neuron matching
- quality assessment
- export/import of tracking results
CATAN is primarily designed for CaImAn output but aims to remain extensible.
Features
- Interactive Qt/VisPy GUI
- Fast visualization of thousands of ROIs
- Across-session neuron tracking
- Rigid and non-rigid remapping
- Sparse matrix support
- HDF5-based project format
- Scriptable Python API
Installation
pip install catan-toolbox[gui]
or
git clone https://github.com/goecidbn/CATAN_toolbox.git
cd CATAN
pip install -e ".[gui]"
CATAN allows for a GUI-less setup, not requiring graphic libraries such as PySide6 and vispy. For most users, the installation including the GUI will be of interest and can be set up via the commands above. For a graphic-less setup, use
pip install catan-toolbox
Running CATAN
catan-gui
or in GUI-less mode:
catan
from catan.gui.app import main
main()
Development
git clone https://github.com/goecidbn/CATAN_toolbox.git
pip install -e ".[gui,dev]"
Run the tests
pytest
Project status
CATAN is currently under active development. The file format and Python API may change until the first stable release.
Citation
If you use CATAN in scientific work, please cite
(paper / DOI once available)
License
MIT License
1 maintainer
Metadata
1 maintainer
Release files for catan-toolbox 0.1.12
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