catan-toolbox 0.1.1

Interactive and algorithmic tools for matching and curating neurons across calcium imaging sessions

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.

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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

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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

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Running CATAN

catan

or

from catan.gui.app import main

main()

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Development

git clone https://github.com/goecidbn/CATAN_toolbox.git
pip install -e ".[gui,dev]"

Run the tests

pytest

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Project status

CATAN is currently under active development. The file format and Python API may change until the first stable release.

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Citation

If you use CATAN in scientific work, please cite

(paper / DOI once available)

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License

MIT License