Creating CATMAID extensions

In the past, anyone wanting to extend CATMAID for their specific use case would need to fork the main repository, making it difficult to take advantage of future improvements to mainline CATMAID, and decreasing utility of the extension to people who may want to make use of it later. Therefore, we have designed the extension system to allow third parties to create external modules which interface with mainline CATMAID without having to change it.

If all that is needed is a modification or extension of front-end code (i.e. no new back-end functionality or database schema changes), it might be enough to configure static front-end extensions. What these are is explained at the end of this section.


CATMAID extensions are python modules which work as Django apps. When that module is made available to the python environment, Django can pick up any database models, API endpoints, and static files associated with the app, and code in the app can interact with code in mainline CATMAID. This modular approach allows much greater interoperability between different versions of CATMAID and the extension.

In the documentation below, we use a fictional extension called myextension.

Installing an Extension

  1. Install the app into your python environment, either by using pip install from PyPI, or cloning the repo and using pip to install from the local

  2. Run python migrate to update the database as necessary. WARNING: it is possible for a migration to irreversibly change or delete data in your existing database.

  3. Run python collectstatic to pick up static files including stylesheets and frontend widgets.

API endpoints should be available at BASE_URL/ext/myextension/...


N.B. CATMAID will only recognise extensions it knows about - i.e. those listed in KNOWN_EXTENSIONS in CATMAID/django/projects/ Check this if it doesn’t seem to be working.

Creating an extension

To quickstart development, you may find this cookiecutter template valuable: clbarnes/CATMAID-ext-cookiecutter. To do it yourself:

  1. Decide on a name! We’ll use myextension here.

  2. Make a branch of CATMAID, adding "myextension" to KNOWN_EXTENSIONS in CATMAID/django/projects/ Make a pull request for this to be included in mainline CATMAID - until then, just use this branch for testing. This should be the only required change.

  3. Create a directory which will hold the module and repository-related cruft (we recommend naming it something obvious like CATMAID-myextension), navigate to it, and then create an empty django app with django-admin startapp myextension

  4. Add an appropriate README, LICENSE,, and so on as laid out in Django’s documentation, in CATMAID-myextension. The manifest and setup files are particularly important.

  5. If your extension includes javascript and/or stylesheets, create myextension/ to make Django Pipeline aware of them. See synapsesuggestor and CATMAID for how they interoperate.

  6. Develop away! For testing purposes, you will need to install the extension in your CATMAID environment - it’s convenient to use pip install -e to install the module in editable mode and python collectstatic -l.

Community Standards

  • See the contributing page.

  • Don’t pick an extension name which may clash with other python modules.

  • Don’t write any migrations which will change data or database tables in the underlying CATMAID installation.

  • Be aware of CATMAID’s namespace - don’t add dependencies or tables which could cause name collisions.

  • As per Django’s guidelines, namespace all static files, templates and so on to your app - e.g. static files should be in a directory called myextension/static/myextension/<files>

Simple front-end extensions

The CATMAID front-end can load extra JavaScript files that are not part of the regular source tree. This allows adding e.g. a new widget or custom analysis code without creating a full extension like explained above. This is sometimes easier and can be configured through three variables in the file.

Which additional files are loaded is defined in the STATIC_EXTENSION_FILES variable, which is expected to be a list of file names. They are expected to be relative to the path defined in STATIC_EXTENSION_ROOT. It is the responsibility of the webserver in use (e.g. Nginx) is expected to map the relative URL path in STATIC_EXTENSION_URL to the STATIC_EXTENSION_ROOT path, which allows the front-end to load the specified files from the static extension URL.