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pyBer v0.1.1 - first public release

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@Andrianarivelo Andrianarivelo released this 23 Jan 14:49
· 166 commits to main since this release
photometry
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Learn about vigilant mode.

pyBer is a desktop GUI for fiber photometry processing with a deterministic core pipeline and an interactive QC workflow.

Highlights

  • Supports raw data in .doric, .h5 or .csv.
  • Artifact detection with global or adaptive MAD and optional padding, plus manual masking
  • Zero-phase low-pass filtering and joint resampling to a target sampling rate
  • Baseline estimation with pybaselines (asls, arpls, airpls)
  • Seven output modes including motion-corrected dFF and z-score variants
  • Fitted-reference motion correction using OLS, Lasso, or robust RLM
  • Export processed traces to CSV or HDF5 with metadata
  • Post-processing: DIO/behavior alignment, PSTH + heatmap, metrics, group mode

Quick start

conda env create -f environment.yml
python main.py
Assets 3
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