Transwell Image Processing Scripts

Description

This repository contains the scripts used for the automated processing, compositing, and visualization of transwell microscopy images from my Bachelor Thesis.

Repository Overview

The repository is structured into three and a half modules:

• ImageJ script/Image_Processing_V1.ijm: An ImageJ macro that automates the batch processing of subdirectories. It locates DAPI, ZO1, and OCCL channel images, applies background subtraction and contrast enhancement, and merges them into a multi-channel composite TIFF and PNG (Merged_Composite.png).
• Image grid maker/image_merger.py: A Python script that searches within a structured directory hierarchy to locate images and stitches them into a 2x2 composite grid.
• Image grid maker/image_merger_finals.py: Same thing, but a bit more flexible.
• Slides viewer/streamlit_app.py: A Streamlit-based interactive web application that uses data_indexer.py to provide a searchable, filterable gallery interface for comparative analysis of the generated composites across multiple conditions, concentrations, and time points.

Setup & Installation

To run the Python scripts in this repository, it is recommended to use a Python virtual environment to isolate dependencies. Activate the virtual environment, then install the packages listed in requirements.txt

Usage

1. ImageJ Batch Processing

This script was designed and run within FIJI Stable Version 2026/03/07-1417 Execute the macro within ImageJ/Fiji:

1. Open ImageJ/Fiji.
2. Navigate to Plugins > Macros > Run... and select Image_Processing_V1.ijm.
3. Choose the root directory containing your raw image subfolders when prompted.

2. Generating Image Grids

Ensure your virtual environment is active. Navigate to the grid maker directory and execute the script:

cd "Image grid maker"
python image_merger.py

Note: The script currently targets the current directory (.). Adjust the TARGET_DIRECTORY variable in the source code if necessary.

3. Running the Slides Viewer Application

Ensure your virtual environment is active. Navigate to the slides viewer directory and launch the Streamlit application:

cd "Slides viewer"
streamlit run streamlit_app.py

This command will start a local web server and open the interactive viewer in your default web browser.