BiScan

Bidirectional scan correction GUI tool for MEMS + Galvano mirror point-scanning microscopes

Overview

BiScan is a GUI application that processes raw TIFF data acquired with a point-scanning microscope combining a MEMS mirror (fast resonant scan) and a Galvano mirror (slow scan).

Each raw frame is split into top and bottom halves:

• Top half: Galvano mirror forward scan
• Bottom half: Galvano mirror reverse scan (flipped vertically for correction)

These are used to perform interleave reconstruction.

Features

Feature	Description
Interleave Preview	Real-time preview of interleaved raw frames (zoom/pan supported)
Z-profile	Time-series plot of average brightness across all interleaved frames
Shift Measurement	Quantify X/Y shift between forward and reverse scans using ECC and phase correlation methods
Save Interleaved TIFF	Export as interleaved multi-page TIFF (BigTIFF compatible); optionally skip the first N frames
Save Shift Figure	Save a figure summarizing shift measurement results and Z-profile
Layout Save	Save and restore window layout to/from file (docking supported)

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Installation

Requirements

• Miniconda or Anaconda
• Windows 10 / 11

Environment Setup (first time only)

Create a dedicated conda environment in the project folder.

conda env create --prefix ".\env" -f environment.yml

Estimated time: 5–10 minutes, Disk usage: ~1–2 GB

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Launching

Double-click run.bat

Or from the command prompt:

cd /d "y:\hayato\Code\Bilateral_correction_GUI"
run.bat

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Usage

1. Open a File

• Menu File > Open Raw TIFF or the Open Raw TIFF... button in the Controls panel
• Number of frames, size, and dtype will be displayed

2. Interleave Preview

• Browse interleaved frames with the frame slider
  • Even index: Top (forward scan)
  • Odd index: Bottom (reverse scan, flipped vertically)
• Mouse wheel to zoom, left drag to pan, double-click to reset
• Toggle displayed frame type with the Top / Bottom checkboxes

3. Z-profile

• Click Compute Z-profile to calculate and plot the average brightness of all frames
• X-axis: interleaved frame number
• Click Auto-scale to auto-adjust axis range

4. Shift Measurement

• Enter the number of frames to average in N frames for avg (0 = all frames)
• Click Measure Shift to run
• Results from both the ECC method (high-precision measurement using time-averaged image) and the phase correlation method (per-frame statistics) are displayed

5. Export

Button	Output File
Save Interleaved TIFF	{original filename}_interleaved.tif
Save Shift Figure	{original filename}_shift_profile.png

• Skip first N interleaved frames: Enter the number of interleaved frames to skip at the beginning before saving. Set to 0 to save all frames (default).
  • Example: set to 4 to discard the first 4 interleaved frames (= first 2 raw frames) from the output file.

6. Layout

• Drag windows by their title bar to move and resize freely
• Windows can be docked together (tabbed or split layout)
• Layout > Save Layout: save the current layout
• Layout > Reset Layout: restore the default layout

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File Structure

BiScan/
├── biscan.py            # Main application
├── run.bat              # Launch script (Windows)
├── environment.yml      # conda environment definition
├── bilateral_gui.ini    # Layout save file (auto-generated)
└── env/                 # conda environment (generated after initial setup)

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Dependencies

Package	Purpose
dearpygui	GUI framework
numpy	Array operations
tifffile	TIFF file read/write
opencv-python	Shift measurement via ECC and phase correlation
matplotlib	Save shift measurement result figures
tqdm	Progress bar for CLI scripts (optional)