LabConstrictor website

Preview: https://cellmigrationlab.github.io/LabConstrictor-Site/

The preview is accessible but has not been officially launched. Its pages tell search engines not to index them; this is not an access restriction. The intended public address is https://labconstrictor.cellmig.org/. Some LabConstrictor guides already link to that address, and app manifests reference its schema URL. Check that the domain works before announcing the launch.

What it does

LabConstrictor packages workflows developed in Jupyter notebooks as installable desktop apps. The notebooks remain the main interface. Authors can also expose selected Python functions in napari, Fiji or QuPath through optional, experimental plugins.

This repository contains the website, not the packaging template or the plugins. It includes:

• an App Centre listing apps built with LabConstrictor, with project pages and downloads for the systems each app supports;
• a How it works guide, from notebook workflow to installer;
• an interactive Demo of an installed app, using a precomputed NucleiSky example (no analysis runs in the browser);
• Docs for installing and using apps, connecting them to image-analysis software, and building and publishing your own;
• an Ecosystem page with the supporting projects and links to related approaches;
• a Submit page explaining how to propose an app for listing.

Most content is edited at its source and imported when the site builds. There are deliberate exceptions: for example, the home-page citation in data/site.yaml repeats the template's citation. The build checks its DOI against the template README, not the entire reference.

Where to edit what

Find the thing you want to change; edit it there, never in the site's generated pages.

To change…	Edit	In repository
A guide for building an app (Docs → Build an app)	.tools/docs/<page>.md; the order and groups are in .tools/docs/README.md	LabConstrictor
The How it works steps and explanations	data/how-it-works.yaml	this repository
The How it works figure and interactive stepper	content/how/, tools/how_figures/crop_preprint_figure.py	this repository
Two user pages that live in the template: Notebook usage after installation, Troubleshooting an installed app	.tools/docs/notebook_usage.md, .tools/docs/troubleshooting_installed_app.md	LabConstrictor
The napari, Fiji or QuPath guide	docs/user-guide.md	LabConstrictor-napari, LabConstrictor-Fiji, LabConstrictor-QuPath
The overview Use apps inside napari, Fiji and QuPath	docs/user-guide.md	LabConstrictor-Tools
The Connect to a microscope guide	docs/smart_microscopy/smart_microscopy.md	NucleiSky
A card on the Ecosystem page (name, summary, status)	docs/labconstrictor-project.yaml (the template's card is inline in data/ecosystem.yaml)	the project's own repository; template exception in this repository
An app's description, declared distribution, supported hosts, icon and screenshots	labconstrictor-app.yaml	the app's own repository
Actual installer files, download URLs and released version	assets and tag of the latest published GitHub Release (resolved by scripts/lcsite/catalogue.py)	the app's own repository; resolved in this repository
Which apps are listed; featured on the home page; shown under Testing and maintenance	registry/<owner>__<repo>.yaml (featured, section: testing)	this repository
The Related projects section of the Ecosystem page	data/related-projects.yaml	this repository
The picture cards on the Use and Build pages	data/hubs.yaml	this repository
Linked image-analysis software and service logos	data/hosts.yaml	this repository
Open and use an app	content/guides/using-apps.md	this repository
Find your problem help page	content/guides/help.md	this repository
Install an app (steps for each system)	.tools/docs/install.md	LabConstrictor
Home page text and the copied LabConstrictor citation	data/site.yaml	this repository
The Submit page	content/submit.md	this repository
The demo page and its home tile (wording)	data/demo.yaml	this repository
The demo's notebook, napari, Fiji and installer views, interactions and styles	content/demo/windows/, content/demo/macos/installer.html, content/demo/demo*.js, content/demo/demo.css, content/demo/installer.css, content/demo/macos.css	this repository
The demo's measured result and microscopy images	content/demo/example.json and images; regenerate with tools/demo_assets/make_demo_assets.py; provenance in content/demo/README.md	this repository
The demo's example installer and matcher settings	content/demo/installer.json and matcher_config.json; regenerate with tools/demo_assets/installer_record.py and matcher_config.py	this repository
The menu	nav: in mkdocs.yml	this repository
The footer, page layout, colours	overrides/, docs/assets/stylesheets/lc.css	this repository
Which projects the Ecosystem page lists	data/ecosystem.yaml (one - repo: owner/name line each)	this repository
Add another guide kept in a repository	one line in data/guides.yaml	this repository
An address that moved (so old links keep working)	one line in data/redirects.yaml	this repository

To list an app, the app's authors use the submission form (or add a pointer file in registry/).

The build/ and site/ directories are generated. These paths under docs/ are also generated and git-ignored: index.md, apps/, guides/, use/, build/, how-it-works/, ecosystem.md, submit.md, demo/, llms.txt and assets/{icons,shots,docs-img,images,hubs,hosts,demo,how}/. Do not edit them by hand: the next build replaces them.

Not everything under docs/ is generated. For example, docs/assets/stylesheets/lc.css, docs/assets/javascripts/lc.js and docs/assets/fonts/ are tracked source files.

When changes appear

The publish workflow runs:

• when changes are pushed to main (pull requests build a preview artifact but do not deploy);
• daily (currently scheduled for 05:23 UTC), to pick up new app releases and changes in other repositories;
• on demand: Actions → Build and publish site → Run workflow.

Successful main and scheduled builds deploy the site; the time it takes depends on GitHub Actions. If a build fails, the previous version stays online. A failed scheduled build opens or updates a GitHub issue.

A missing or invalid guide, required picture or ecosystem project file stops the build. App catalogue failures are different: if an individual app's manifest or release cannot be resolved, that app is omitted and the reason is recorded in build/problems.md. Pull-request builds fail when any registered app is omitted; main and scheduled builds can publish the remaining apps. A scheduled build also opens or updates an issue about omitted apps.

Going public

In mkdocs.yml, extra: listed: false adds noindex instructions to the pages, creates an empty sitemap and writes a disallowing robots.txt. These are indexing instructions, not access controls. On the GitHub Pages project URL, the generated robots.txt is not at the host root, so the page-level noindex instruction is especially important.

At launch, confirm the custom domain and the links already pointing to it, update site_url, and set extra: listed: true.

For developers and agents

Read AGENTS.md: how the site is built, the coding rules (they are checked by the tests), and how untrusted input is handled. DESIGN.md says how every kind of title, link, button, card and image must look and behave.

Licence

• Site code (scripts/, tests/, tools/, overrides/, styles and scripts): MIT, see LICENSE.
• Original text written for this site: CC BY 4.0, where the site's authors own the rights.
• Microscopy images in the demo: derived from a CC BY 4.0 dataset. Its attribution, modifications and provenance are described in content/demo/README.md. This does not automatically license other artwork in the demo.
• LabConstrictor logo and comic: licensing terms have not yet been stated. The NucleiSky app icon used in the demo also has rights still to be confirmed; do not assume it shares the microscopy dataset's licence.
• Material imported from other repositories retains its original licensing and attribution requirements. An image or logo does not necessarily share its repository's code licence.
• Fonts: Inter and Bricolage Grotesque are under the SIL Open Font License; see docs/assets/fonts/. Logos of other software and services belong to their respective owners and are shown to identify them.