The gallery: site.yaml

site.yaml describes the landing gallery and the chrome around the viewer: a title and intro, the datasets and their cards, an optional navigation bar, and where the bundles are hosted. spatialscape site build site.yaml turns it into datasets.json next to the viewer's index.html, which is what the gallery reads. You edit the yaml; the JSON is a build output.

title: LIBD spatial data browser
intro: Published spatial transcriptomics and snRNA-seq datasets, viewable in the browser.
nav:
  title: spatialscape
  logo: logo.svg
  links:
    - { label: Docs, url: https://mictott.github.io/spatialscape/docs/ }
    - { label: GitHub, url: https://github.com/MicTott/spatialscape }
# data_url: https://data.example.org          # bundles live there at <data_url>/<id>; the site carries only the viewer
datasets:
  - config: amygdala.yaml                      # a dataset yaml: built into bundles/amygdala next to it when needed
    paper: { title: Totty et al., url: https://doi.org/... }
    tags: [amygdala, visium, xenium]
  - bundle: ../dlpfc/bundles/dlpfc             # an already built bundle
    description: Thirty sections across ten donors.   # replaces the manifest's description on the card
  - id: hippocampus                            # a placeholder card
    name: Human hippocampus
    description: Coming later this year.
    platforms: [visium, snrnaseq]

spatialscape site init writes this file for the yamls and bundles you name, or for every dataset yaml and bundles/* folder next to it when you name none.

Dataset cards

Each entry is exactly one of config: (a dataset yaml), bundle: (a built bundle) or id: (a placeholder, which also needs name:). Everything the gallery shows comes from the bundle's manifest (name, description, platforms, sample and cell counts, gene count, thumbnail); these keys add to or replace it.

Key	Meaning
name, description	card text; default: the dataset's own
paper	{ title, url } shown under the description
tags	short labels
status	live, local or coming soon (the badge); default live, placeholders coming soon
accent	color of the generated card art when there is no thumbnail
thumbnail	image URL; default <bundle>/thumbnail.png, which build renders
platforms	placeholders only; bundles report their own

The navigation bar

When nav is present, a slim bar appears above the viewer and the gallery: its title links to the gallery, a dataset switcher lists every card that has a bundle, and links are rendered on the right. Without nav the viewer has no chrome above the map, which is right for embedding it in another page.

What the viewer reads

datasets.json is plain JSON: title, intro, site (the nav block) and datasets, one object per card with id, name, description, platforms, samples, cells, genes, url (empty for placeholders), status, thumbnail, paper, tags and accent. ?d=<id> opens a card by id and ?d=<url> opens any bundle anywhere.

spatialscape serve <folder> generates the same document on the fly for a folder of bundles, and spatialscape site build <folder> writes it without any settings, which is all a single dataset needs. If you keep publication metadata elsewhere, generate site.yaml from it so a dataset is entered once.