BMI567 Final Project - Phoebe

This repository contains the code, selected data subset, and generated results for the BMI567 final project on automated measurement of Candida albicans filament length from 40X TIFF microscopy images.

Environment

Python 3.10 or newer.

requirements.txt contains the required packages.

Repository Description

• config.json: Project configuration.
• data/selected_subset.csv: Data for the 60 selected images.
• data/raw_selected/: The 60 TIFF images used in the project and their paired CSV annotations.
• src/: Python source code for segmentation, measurement and evaluation.
• results/tables/: Generated automated measurements and evaluation metrics.
• results/figures/: Result figures.
• run_final_analysis.ps1: Re-runs the four final methods and rebuilds the comparison figures.
• run_with_project_python.ps1: Helper script for running Python scripts from PowerShell.

Getting Results

.\run_final_analysis.ps1

This regenerates the final measurements, evaluation tables, and result figures for the four reported methods:

1. Global Otsu thresholding
2. Adaptive local thresholding
3. Otsu with distance-transform body detection and skeleton pruning
4. Paper-inspired cell-body-to-tip graph measurement