Welcome to suite2p’s documentation!
suite2p is an imaging processing pipeline written in Python 3 which includes the following modules:
Registration
Cell detection
Spike detection
Visualization GUI
For examples of how the output looks and how the GUI works, check out this twitter thread.
This code was written by Carsen Stringer and Marius Pachitariu. For support, please open an issue.
The reference paper is here. The deconvolution algorithm is based on this paper, with settings based on this paper.
We make pip installable releases of suite2p, here is the pypi. You
can install it as pip install suite2p
Basics:
- Installation
- Inputs
- Settings (ops.npy)
- Using the GUI
- Outputs
- Multiday recordings
- Developer Documentation
- Frequently Asked Questions
How it works:
API:
- suite2p.io package
- suite2p.registration package
- suite2p.detection package
- Submodules
- suite2p.detection.anatomical module
- suite2p.detection.chan2detect module
- suite2p.detection.denoise module
- suite2p.detection.detect module
- suite2p.detection.metrics module
- suite2p.detection.sourcery module
- suite2p.detection.sparsedetect module
- suite2p.detection.stats module
- suite2p.detection.utils module
- Module contents
- suite2p.extraction package
- suite2p.classification package
- suite2p.gui package
- Submodules
- suite2p.gui.buttons module
- suite2p.gui.classgui module
- suite2p.gui.drawroi module
- suite2p.gui.graphics module
- suite2p.gui.gui2p module
- suite2p.gui.io module
- suite2p.gui.masks module
- suite2p.gui.menus module
- suite2p.gui.merge module
- suite2p.gui.reggui module
- suite2p.gui.rungui module
- suite2p.gui.traces module
- suite2p.gui.utils module
- suite2p.gui.views module
- suite2p.gui.visualize module
- Module contents