Daniel-Waiger / automated-spheroid-detection

Automated Spheroid Detection in Fiji/ImageJ

Overview

This macro automates the process of detecting spheroids and analyzing live/dead ratios in merged .tif images. It iterates through images in a specified directory, processes each one, and saves the results. The merged images were created with Dual-Channel-Fluorescence-Image-Merger-with-Filename-Truncation.

Example - From Left to Right: Raw → 8-bit Gray (after conversion from composite to RGB) → Cellpose Label Image.

Pre-requisites

• Fiji (ImageJ) Installation
• Cellpose Installation

Plugins and how to install them:

• BIOP Cellpose Wrapper Manual - to use Cellpose Advanced in Fiji.
  • How to install plugins in Fiji
  • Fiji FAQ - Quick How-to Manual

Usage Instructions

1. Start the Macro

1. Open Fiji (ImageJ).
2. Open the script editor (Plugins > New > Macro).
3. Copy and paste the provided macro code into the editor.
   • Or, you can drag-and-drop the macro file onto Fiji's main toolbar, automated-spheroid-detection.ijm.

5. Run the macro (Run button in the script editor).

6. When prompted, Choose the directory containing your merged .tif image files.
7. Monitor the console for progress logs.
8. Results: After completion, the measurements will be saved in CSV files within the selected directory, and ROIs will be saved as .zip files.

Notes

• Adjust Calibration: Modify pixelWidth and pixelHeight values to match your microscope's calibration.
• Cellpose Parameters: Customize the parameters in the Cellpose Advanced function to suit your specific sample type and detection requirements.
• Output: Ensure the directory has write permissions to save results correctly.