Introduction

MIA can either be installed into Fiji via the ImageJ Updater (Option 1) or manually using the latest releases on GitHub (Option 2). For day-to-day use, installing from Fiji is recommended, whereas the GitHub route allows specific versions of MIA to be used. If problems are encountered, please see the troubleshooting page. For any issues not covered on the troubleshooting page, you can submit an issue via GitHub.

Option 1: Installing directly from Fiji

The latest version of MIA can be installed directly into Fiji via an update site.

  1. Launch the ImageJ Updater from Help > Update...
  2. Click "Manage update sites" and in the window that opens, click "Add update site"
  3. In the blank row that appears, enter the following:
    • Name: ModularImageAnalysis
    • URL: https://sites.imagej.net/ModularImageAnalysis
  4. Whilst still on the "Manage update sites" window, tick the "IJPB-Plugins" update site
  5. Close the "Manage update sites" window, then click "Apply changes".

Option 2: Installing manually from GitHub

Specific versions of MIA can be downloaded from GitHub and installed into Fiji manually. Note: If installing MIA manually, the ModularImageAnalysis update site should be disabled from the ImageJ Updater.

  1. Download the desired version of MIA from the Releases page.
  2. Place this .jar file into the /plugins directory of the your Fiji installation.
  3. Install MorphoLibJ using the instructions here.

What next?!

You're now ready to start using MIA. You can learn about the two interfaces in the Processing view and Editing view guides. For instructions on running pre-prepared workflows (distributed as .mia files) please see the Using existing workflows guide. Alternatively, you can find instructions on developing new workflows in the Creating workflows guide.

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