Mouse Brain CFOS Analysis

This script is designed to analyze mouse brain sections for CFOS based on Stardist DAPI nuclei segmentation.

DOI:

Author

Daniel Waiger

• Email: [email protected]

• Image.sc forum: Daniel_Waiger

• Institution: CSI – Center for Scientific Imaging at The Robert H. Smith Faculty of Agriculture, Food and Environment of the Hebrew University of Jerusalem

• Website: Faculty of Agriculture CSI Microscopy

Description

Dialogs and GUIs

Script steps

The script performs the following steps:

1. Opens the selected image file.
2. Performs a sum projection of the image.
3. Splits the image into channels.
4. Applies LUTs (Look-Up Tables) to the channels.
5. Prompts the user to select an ROI (Region of Interest) or processes the entire image.
6. Processes the selected channels.
7. Runs StarDist segmentation on the DAPI channel.
8. Saves the results and ROI sets.
9. Prints the total run time.

Requirements

• ImageJ/Fiji
• Bio-Formats Plugin
• StarDist Plugin

Installation

1. Install ImageJ/Fiji from the official website.
2. Install the Bio-Formats plugin.
   • To load .ims files and select the Resolution Level (Defined as Series in the script).
3. Install the StarDist plugin.

Both plugins can be installed via the Help Menu --> Update... --> Manage Update Sites

Usage

1. Open ImageJ/Fiji.
2. Load the macro script into ImageJ/Fiji.
3. Run the script.
4. Follow the prompts to select the image file, save directory, channel names, and ROI selection.

Mouse Brain CFOS Analysis Script Flowchart

graph TD
    A[Start Script] --> B[Close all open images]
    B --> C[Collect user-defined parameters]
    C --> D{Validate inputs}
    D -->|Invalid| E[Exit: No image file, .ims, or output directory selected]
    D -->|Valid| F[Open image and set measurements]
    F --> G[Perform sum projection]
    G --> H[Split channels]
    H --> I[Apply LUTs to split images]
    I --> J{Select ROI?}
    J -->|Yes| K[Prompt user to select ROI]
    K --> L[Confirm and save ROI selection]
    L -->|Confirmed| M[Process selected ROI]
    J -->|No| N[Process entire image with the risk of crashing
 Fiji when loading big images]
    M --> O[Process Channel 1]
    N --> O[Process Channel 1 + 2]
    O --> P[Run StarDist segmentation on Channel 1]
    P --> Q[Measure Channel 2 with Stardist Labels]
    Q --> R[Save results and ROI sets]
    R --> S[Clear Results table]
    S --> T[Print total run time]
    T --> U[End Script]

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