GutMorphometry

Fiji/ImageJ macro and Python helper scripts for semi-automated morphometry of mouse gut Swiss-roll H&E sections.

The tool measures:

• villus height
• villus width
• villus area
• crypt depth
• muscularis thickness

The Fiji macro handles the interactive workflow and ROI collection. Python scripts perform the image-processing steps used for villus width and muscularis thickness QC.

Repository Layout

fiji/
  plugins/
    Gut_Morphometry.ijm
  scripts/Plugins/AutoRun/
    musc_thickness.py
    tune_muscularis.py
    villus_width.py
docs/
  GutMorphometry_Guide.md
requirements.txt

Requirements

• Windows 10/11
• Fiji/ImageJ
• Python 3.8 or later
• Python packages listed in requirements.txt

Install the Python dependencies with:

pip install -r requirements.txt

Installation

Copy the files into a Fiji installation:

fiji/plugins/Gut_Morphometry.ijm
  -> [Fiji.app]/plugins/Gut_Morphometry.ijm

fiji/scripts/Plugins/AutoRun/*.py
  -> [Fiji.app]/scripts/Plugins/AutoRun/

Then edit g_python_cmd near the top of Gut_Morphometry.ijm if Fiji cannot find your Python executable through PATH.

Workflow Summary

Open a gut section image in Fiji and run:

Plugins > Gut Morphometry [G]

The expected image filename format is:

[AnimalID]_[Region]_[Section].tif

Region codes:

• U: upper small intestine
• M: mid small intestine
• L: lower small intestine
• C: colon

Output files are written next to each image, usually in an image-specific subfolder:

• *_results.csv
• *_coords.jsonl
• *_outer_V*_villus.png
• *_outer_MU*_muscularis.png
• *_overlay.jpg

See docs/GutMorphometry_Guide.md for the full Japanese user guide and algorithm notes.

Notes

This repository intentionally excludes raw microscopy images and generated analysis outputs. Keep large .tif, .png, .jpg, .csv, and .jsonl result files outside Git unless they are deliberately curated as examples.

License

MIT