GUI Usage Guide

Main Page

The main page provides a complete workflow for analyzing individual kymograph files.

File Table

• Single Selection: Click a row to select a file
• Columns: File name, folder info, analysis status, metadata preview
• Status Indicators: ✓ marks show if file is analyzed and saved

Image & Line Viewer

• Kymograph Display: Shows the 2D kymograph image
• Line Plot: Shows velocity over time from analysis
• Zoom/Pan: Use mouse to zoom and pan the image
• Contrast Controls: Adjust intensity scaling

Metadata Forms

• Experimental Metadata: Edit species, region, cell type, depth, branch order, direction, sex, genotype, condition, and notes
• Olympus Header: View acquisition parameters (read-only)
• Analysis Parameters: View analysis settings and results (read-only)

Analysis Toolbar

• Window Size: Select analysis window size (16, 32, 64, 128, 256)
• Analyze Flow: Run Radon-based flow analysis
• Cancel: Stop running analysis
• Save: Save analysis results to disk

Batch Page

The batch page allows processing multiple files sequentially.

Multi-Selection

• Select Multiple Files: Click multiple rows to select them
• Selection Counter: Shows number of selected files
• Analyze Selected: Process only selected files
• Progress Tracking: See progress for both individual files and overall batch

Batch Controls

• Window Size: Set analysis window size for all files
• Analyze Flow: Start batch processing
• Cancel: Stop batch processing at any time

Tips

• Use the folder selector to switch between different data directories
• Analysis results are saved in a -analysis subfolder alongside your TIFF files
• The GUI preserves your file selections when navigating between pages
• Use the contrast controls to better visualize flow patterns in the image