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
🚀 Version 3.0 — Latest stable release

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
• Brightness & Contrast (BnC): adjust image display settings
• ROI tools: draw elliptical ROIs, freehand drawing tool, translate or rotate ROIs, move multiple ROIs, save/load as JSON, quick-select saved ROIs
• Metadata viewer: inspect experiment metadata directly in the application
• Second-level analysis viewer: explore and visualize second-level analysis results
• 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

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.

Installation

Phasor Handler is now available on PyPI and can be installed via pip or from source using Conda/Mamba.

Option 1: Install via pip (Recommended)

The easiest way to install Phasor Handler is through pip:

pip install phasor-handler

After installation, you can run the application:

phasor-handler

PyPI Package: https://pypi.org/project/phasor-handler/

Option 2: Install from source (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 into it:

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

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

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)

If installed via pip:

pip install --upgrade phasor-handler

If installed from source:

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

cd Phasor-Handler
git pull --ff-only