meanap.catnap.denoising

Denoising pipeline for suite2p fluorescence traces.

Ported from Functions/twoPhoton/denoiseSuite2pData.py.

Requires:

• pybaselines (baseline estimation)

• scipy (signal processing, peak detection)

• oasis (OASIS deconvolution — optional; install from

  https://github.com/j-friedrich/OASIS if needed)

Functions

oasis_available()
process_suite2p_folder(suite2p_dir[, ...])	Run the full denoising pipeline on one suite2p/plane0 directory and save outputs as .npy files alongside the inputs.

meanap.catnap.denoising.oasis_available()

Return type:

bool

meanap.catnap.denoising.process_suite2p_folder(suite2p_dir, overwrite=False, denoising_threshold=1.3, time_before_peak_s=1.0, time_after_peak_s=2.05, denoising_width_sec=1.13, denoising_wlen_sec=12.0)

Run the full denoising pipeline on one suite2p/plane0 directory and save outputs as .npy files alongside the inputs.

Outputs written:

Fdenoised.npy, timePoints.npy, peakStartFrames.npy, peakEndFrames.npy, peakHeights.npy, eventAreas.npy

Parameters:

• suite2p_dir (str | Path)

• overwrite (bool)

• denoising_threshold (float)

• time_before_peak_s (float)

• time_after_peak_s (float)

• denoising_width_sec (float)

• denoising_wlen_sec (float)

Return type:

None