This page explains how to write and edit wiki pages. The simplest way to create or modify a page is using GitHub’s online file editor. Each page has an “Edit page” link at the top right with a direct link to this interface.

Advanced users can make edits via a local clone of the site repository; see the advanced editing guide for setup instructions.

Requirements

As this wiki is completely hosted on GitHub, you will need to be logged into a GitHub account to make edits (this replaces the old system of registering for an ImageJ-wiki-specific account). If you don’t have an account yet, you can create one freely.

When making edits through the GitHub web UI, first-time contributors will likely be prompted to fork this repository. Make your edits to your fork as described below, and then create a pull request.

An admin will review your pull request, merge it, and add you as a collaborator. Any future edits can then be made directly to this wiki. You can delete your fork at that point.

You can also manually create forks at any time, and are welcome to continue using the Pull Request mechanism if you prefer.

Creating a new page

Let’s dive in to how to create a new page on the site. If you are looking to edit an existing page, skip to adding and editing page content below. See also the general GitHub guide to editing files.

1. Navigate to an appropriate sub-directory of the pages section of the repository. For example, if you are creating a page about a plugin, you would go to _pages/plugins/. Note: if you need to create a new sub-directory, it can be specified in the file name below.

2. Click Add file then Create new file from the drop-down:

   

3. Add a name for your file. Note: this is not the page title; the page title will be applied in the next section, front matter. File names should be:

   • all lower case
   • use the file extension .md
   • optionally prefixed with new sub-directory name(s), separated with /
   • avoid symbols and spaces, and separate words using dashes (-):

   

Front matter

Every page begins with a block of front matter: a sequence of parameters that configure your page. Without the front matter, your page will not render correctly. The following table lists front matter fields you can use:

Below is a minimal example front matter block. You can copy and paste this code into the editor of a new page (see above).

Replace My Awesome Page with the title for the new page.

---
title: My Awesome Page
---

Adding + editing page content

This section covers how to populate the content of your page.

Markdown

Markdown is plain-text syntax formatting, allowing you to easily and cleanly modify text with italics, bold, ordered or bulleted lists, etc. This wiki, as a Jekyll site, uses kramdown. A quick-reference can be found here, and a general Jekyll support reference here. Also helpful is GitHub Flavored Markdown (GFM) guide found here.

Here are some common kinds of text formatting:

Note that the last example, colored text, is not really Markdown, but rather plain HTML. However, Markdown does not have a syntax for changing text color, and it supports mixing in HTML, so you can use the technique above if you need text in different colors.

Here are some common image uses:

Image	Markup
	
	{:width="64px"}

Note that the last example includes inline styling, which is kramdown-specific.

Certain kinds of structures have dedicated pages of this guide:

• Images (using Liquid, not Markdown, for more complex image needs such as galleries, figures, etc…)
• Tables
• Math expressions
• Source code and syntax highlighting
• Footnotes

Liquid

On top of Markdown, the site uses a templating language called Liquid to make page editing more convenient than with Markdown alone. Liquid tags look like {% ... %} or {{ ... }}. Many pages on this site use Liquid to invoke functions called includes, which enable insertion of images, figures, notices, and more. (Think of this as: “I would like to include an image”.) Here are a couple of examples:

Markup	Result
{% include icon name="imagej" %}
{% include person id="rasband" %}	Wayne Rasband

Available includes

The following tables list all of this site’s general-purpose includes:

Citations and footnotes

Linking

Symbols

Media

Notices

Source code

Miscellaneous

MARKED FOR REMOVAL

Finalizing your edits

Once you’re happy with your new page, click on the “Commit changes” button to save your work:

This will bring up a dialog where you can set the summary commit message, a more in-depth description of the changes, and verify the account used to make the changes.

For most edits it makes sense to simply commit to the main branch directly. Just adding pages won’t break anything. But if you are concerned you can always use the “branch and pull request” option. Just make sure to assign or mention someone in the PR (pull request)! Otherwise we may not see it to merge it in a timely manner. Good options for reviewer are Mark Hiner and Curtis Rueden.

If you aren’t sure what to write in your commit message, there are many guides out on the internet. You can even ask ChatGPT! Just don’t do this:

Once you are sufficiently happy with your message and click the “Commit changes” button, your edits will go onto the history of the site. This will trigger a rebuild of the site. Once that completes, your changes will show up on the live site! Thank you for your contribution!

Adding non-page files

If you need to add other types of files, you can use the “Upload files” option in the “Add files” button:

This will bring you to a drag-and-drop interface that allows you to create a new commit directly after you’ve uploaded your desired files.

If you want more control over the structure of the files you’re adding, it may be easier to go the Advanced Editing route. This also allows you to preview your changes before committing them.

FAQ

Why do I need to fork this repository to edit it?

If you go to edit a page and see this message, it means you are not listed as a collaborator in this repository.

Proceed with the forking as indicated (which creates a copy of the repository under your account, so that you can edit it). Make the edits you’d like to your fork, then submit a pull request. Upon completion of the pull request review you will be made a collaborator and can make future edits directly.