phasor-handler 3.0.0

A PyQt6 GUI toolbox for processing two-photon phasor imaging data

Phasor-Handler (Windows)

Phasor Handler is a toolbox for processing raw two-photon phasor imaging data: convert → register → explore → extract calcium traces.
It provides a PyQt6 GUI for viewing registered or raw stacks (Ch1/Ch2), z-projections (std/max/mean), drawing/storing ROIs, overlaying stimulated ROIs from metadata, and exporting ROI traces.

⚠️ Platform: Windows 10/11 only
🧪 Status: actively developed (Brightness & Contrast dialog is WIP)

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Features

• Load registered TIFF (Ch1-reg.tif, Ch2-reg.tif) or raw NPY fallbacks (ImageData_Ch0_TP0000000.npy, ImageData_Ch1_TP0000000.npy)
• Linear and non-linear motion-correct TIFF images using Suite2p
• Automated cell detection using Suite2p
• Channel switching (Ch1/Ch2) and Composite (G/R)
• Z-projections: standard deviation, max, mean
• ROI tools: draw elliptical ROIs, translate or rotate ROIs, save/load as JSON, quick-select saved ROIs
• Stimulus overlay: show stimulated ROI locations from experiment metadata and add to the saved ROIs
• Trace plotting: configurable formula, custom y-limits, frame/time (s) x-axis
• Export: write per-ROI traces for all frames to .txt (tab-separated)
• Keyboard: R save/add ROI, Delete remove selected ROI, Esc clear selection, Alt+S load stimulated ROIs, Right Click + drag translate selected ROI, Y toggle right click to rotation mode

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Input data layout

For each dataset directory, Phasor Handler looks for any of:

• Ch1-reg.tif
• Ch2-reg.tif # optional
• ImageData_Ch0_TP0000000.npy # raw fallback for Ch1
• ImageData_Ch1_TP0000000.npy # optional raw fallback for Ch2
• experiment_summary.pkl # optional metadata (or .json)

Registered TIFFs are preferred when available; raw NPYs are used as fallback.

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Installation (Windows, Conda)

This project provides an environment.yml for Windows. The environment is large (GUI, image I/O, napari/suite2p), so mamba is recommended, but conda works too.

1) Install Conda/Mamba (if needed)

• Install Miniconda or Mambaforge on Windows.
• (Optional) Add mamba for faster solves:

  conda install -n base -c conda-forge mamba
  

2) Get the code

• Clone the repo and change it into

  git clone https://github.com/joshemuel/Phasor-Handler.git
  chdir Phasor-Handler
  

• Alternatively, you can download the entire project as a zip file, unzip it, then open that directory in Miniconda cd Phasor-Handler

3) Create the environment

• Using mamba:

  mamba env create -f environment.yml
  

• Using conda:

  conda env create -f environment.yml
  

4) Activate and run

• Before running the toolbox, activate the environment

  conda activate suite2p
  python app.py
  

Update (Windows, Conda)

1) Go to your local repo and pull the latest code from the branch you use

chdir Phasor-Handler
git pull --ff-only