Laminario, an Open Collection of Microscope Slides in the Spirit of iNaturalist
A public collection where every case is a real microscope slide shown as the glass object it is, its format and size, the specimen under the coverslip, a printed label with a scannable QR, and behind the glass the micro imagery, from one photomicrograph to a whole-slide scan with focal planes and polarised pairs, explored in deep zoom over IIIF. Three realms, 18 collections and 130 sub-collections and groups with their own iconography; visitors browse without an account, invited contributors add slides, the community agrees on identifications. Version 0.17.002: seventeen units released and deployed since 2026-09-30 at laminario.ml.fasl-work.com, with a base collection of 505 slides (786 images) from open sources, shown as realistic glass slides in 3D. Lifecycle planned.
Business Context
For a visitor the promise is to look at a slide as an object and then put it on the stage: objectives derived from the pixel size, a scale bar in real units, focal planes, polarised pairs and rotation for rocks and minerals, and a label whose QR opens the slide's page. For a teacher or a collection, the promise is a place where a slide can be added with its provenance, licence and author per asset, identified by a two-thirds agreement rule, and served as a standard IIIF manifest rather than locked in one viewer.
Strategic Value
Laminario is being built in the mandatory order: seven research dossiers, an architecture decision (ADR-0077), a software design document with a named verification gate per requirement, the plan validated by Felipe on 2026-09-24, and then the units. Version 0.01.000 (2026-09-25) was the repository base and the data model with both contracts. On 2026-09-28 and 29 the units followed in order, each with its verdict page, up to 0.15.000: the imaging engine, delivery over IIIF, the worker, resumable uploads, invitation-only accounts, the collection tree, a base collection of 505 slides over the 18 collections (Wikimedia Commons, the Natural History Museum's Data Portal, Smithsonian Open Access, Zenodo's NMNH focal stacks, the OpenSlide test data; 14 whole-slide scans and a registered polarised pair for every rock family, each image with its licence, author, source record and SHA-256), the product's own visual system, Explore, the slide and its stage, Contribute, Identify with iNaturalist's community-taxon rule read from its source, the cabinet with label sheets printed at 1:1, and About. The deployment (0.16.000, 2026-09-30) runs the API, the worker, the upload server and the tile server on the ML VPS behind HTTPS, with the base collection imported and checked file by file against its bake, and a production gate of 22 checks passing against the live site. The glass-slide interface (0.17.000) draws every set of the collection as realistic glass slides in 3D, at each slide's own format, with the photograph of the real glass where a scanner stored one, in four arrangements the visitor chooses (a carousel, a filing-cabinet drawer, a slide box, a folder), keyboard-navigable and drawn flat where WebGL is missing; 0.17.002 shows one real slide from each collection on the landing. The lifecycle is planned.
The Challenge
Microscope slides are among the most numerous objects in natural-history and teaching collections; the Natural History Museum in London alone holds about 2.5 million. A growing share is digitised and openly licensed, but it is published as records in museum portals or as files in data deposits: nobody can browse slides as slides, across plants, animals, microbes, rocks, minerals and crystals, or add their own. The whole-slide files are multi-gigabyte scanner formats (NDPI, SVS, MRXS, DICOM) that ordinary web tooling cannot open.
Our Approach
A FastAPI API over SQLite with full-text search and invitation-only accounts; a separate worker claiming durable jobs from the same database; libvips with OpenSlide writing one pyramidal BigTIFF per image plane; the IIIF Image API 3 at level 2 from iipsrv behind an nginx cache, plus a IIIF Presentation 3 manifest per slide so any IIIF viewer can open it; resumable uploads through tusd with quarantine, sniffing, checksum and quotas; a React and TypeScript frontend with OpenSeadragon for the stage and MapLibre over a self-hosted PMTiles basemap for the places. The base collection of at least 300 openly licensed slides (NHM, Smithsonian Open Access, Zenodo, Wikimedia Commons, CDC PHIL) is ingested through the same pipeline as a contributor's upload. The product carries its own original design system: the shared CAOS shell is excluded by Felipe's instruction.
Key Performance Indicators
| KPI | Baseline | Result | Impact |
|---|---|---|---|
| A slide as an object, not a record | A row in a museum portal or a file in a deposit | True format and size, the macro image under the coverslip, a printed label with a scannable QR, then the micro assets: single images, deep-zoom pyramids, focal planes, polarisation states | The thing on the screen is the thing in the drawer |
| A collection tree with its own iconography | One taxonomy for life, nothing for rocks and crystals | Three realms (life, earth, matter), 18 collections, 130 sub-collections and groups, 186 hand-drawn icons, placement rules anchored on GBIF, the IMA mineral list, crystal systems and materials | Plants, microbes, thin sections and crystals sit in one cabinet |
| Standards on the way out | Imagery locked in one viewer | IIIF Image API 3 level 2 tiles and a IIIF Presentation 3 manifest per slide; source, author and licence per asset; resumable uploads of multi-gigabyte scanner files | Any IIIF viewer can open a Laminario slide |
Architecture
laminario pipeline
Technology Stack
Visual assets for this project are not publicly available.