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

• Module Index

• Search Page

• Index

Basics:

• Installation
  • Dependencies
• Inputs
  • Input format
    • Directory structure
    • Frame ordering
    • Recordings with photostim / other artifacts
  • Different file types
    • Tiffs
    • Bruker
    • Mesoscope tiffs
    • Thorlabs raw files
    • HDF5 files (and *.sbx)
    • sbx binary files
    • Nikon nd2 files
  • BinaryRWFile
• Settings (ops.npy)
  • Main settings
  • File input/output settings
  • Output settings
  • Registration settings
    • 1P registration
    • Non-rigid registration
  • ROI detection settings
    • Cellpose Detection
  • Signal extraction settings
  • Spike deconvolution settings
  • Classification settings
  • Channel 2 specific settings
  • Miscellaneous settings
• Using the GUI
  • Different views and colors for ROI panels
    • Views
    • Colors
    • Correlations
    • Correlations with 1D var
    • Rastermap / custom
  • Buttons / shortcuts for cell selection
    • Mouse control
    • Keyboard shortcuts
    • Multi-cell selection
  • Trace view (bottom row)
  • Classifying cells
    • Adding data to a classifier
    • Building your own classifier
  • Visualizing activity
  • Manual adding of ROIs
  • Merging ROIs
  • View registered binary
    • Z-stack Alignment
  • View registration metrics
• Outputs
  • MATLAB output
  • NWB Output
  • Multichannel recordings
  • stat.npy fields
  • ops.npy fields
• Multiday recordings
• Developer Documentation
  • Versioning
  • Testing
    • Downloading Test Data
    • Running the tests
• Frequently Asked Questions
  • Cropped field-of-view
  • Deconvolution means what?
  • Multiple functional channels
  • Z-drift
  • No signals in manually selected ROIs

How it works:

• Registration
  • Finding a target reference image
  • Registering the frames to the reference image
  • 1. Rigid registration
  • 2. Non-rigid registration (optional)
  • Metrics for registration quality
    • CLI Script
• Cell Detection
  • Summary
  • SVDs ( = PCs) of data
  • Sourcery
• Signal extraction
• Spike deconvolution

API:

• suite2p.io package
  • Submodules
  • suite2p.io.binary module
  • suite2p.io.h5 module
  • suite2p.io.nd2 module
  • suite2p.io.nwb module
  • suite2p.io.save module
  • suite2p.io.sbx module
  • suite2p.io.server module
  • suite2p.io.tiff module
  • suite2p.io.utils module
  • Module contents
• suite2p.registration package
  • Submodules
  • suite2p.registration.bidiphase module
  • suite2p.registration.metrics module
  • suite2p.registration.nonrigid module
  • suite2p.registration.register module
  • suite2p.registration.rigid module
  • suite2p.registration.utils module
  • suite2p.registration.zalign module
  • Module contents
• suite2p.detection package
  • Submodules
  • suite2p.detection.anatomical module
  • suite2p.detection.chan2detect module
    • cellpose_overlap()
    • correct_bleedthrough()
    • detect()
    • intensity_ratio()
    • quadrant_mask()
  • suite2p.detection.denoise module
  • suite2p.detection.detect module
  • suite2p.detection.metrics module
  • suite2p.detection.sourcery module
    • circleMask()
    • connected_region()
    • create_neuropil_basis()
    • drawClusters()
    • extendROI()
    • getSVDdata()
    • getSVDproj()
    • getStU()
    • getVmap()
    • get_connected()
    • get_stat()
    • iter_extend()
    • localMax()
    • localRegion()
    • minDistance()
    • morphOpen()
    • pairwiseDistance()
    • postprocess()
    • r_squared()
    • sourcery()
    • sub2ind()
  • suite2p.detection.sparsedetect module
    • EstimateMode
    • add_square()
    • estimate_spatial_scale()
    • extendROI()
    • extend_mask()
    • find_best_scale()
    • iter_extend()
    • multiscale_mask()
    • neuropil_subtraction()
    • sparsery()
    • square_convolution_2d()
    • two_comps()
  • suite2p.detection.stats module
    • EllipseData
    • ROI
    • aspect_ratio()
    • count_overlaps()
    • distance_kernel()
    • filter_overlappers()
    • fitMVGaus()
    • mean_r_squared()
    • median_pix()
    • norm_by_average()
    • roi_stats()
  • suite2p.detection.utils module
    • downsample()
    • hp_gaussian_filter()
    • hp_rolling_mean_filter()
    • mask_ious()
    • mask_stats()
    • match_masks()
    • square_mask()
    • standard_deviation_over_time()
    • temporal_high_pass_filter()
    • threshold_reduce()
  • Module contents
• suite2p.extraction package
  • Submodules
  • suite2p.extraction.dcnv module
    • oasis()
    • oasis_matrix()
    • oasis_trace()
    • preprocess()
  • suite2p.extraction.extract module
  • suite2p.extraction.masks module
    • create_cell_mask()
    • create_cell_pix()
    • create_masks()
    • create_neuropil_masks()
  • Module contents
• suite2p.classification package
  • Submodules
  • suite2p.classification.classifier module
  • suite2p.classification.classify module
  • Module contents
• 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