Powers of Life

A microscope's-eye journey through scale. Slide across the physical size (µm, log scale) of real bioimaging datasets shared via the SSBD:database, from single molecules to whole tissues.

Two views, sharing the same data:

• Horizontal view — a horizontal scale slider; moving it slides the current image/metadata off to one side while the next one emerges from the other.
• Zoom view — the slider sets the field of view, and each image is drawn at its true size relative to it, so moving the slider zooms continuously from one dataset into the next, with a scale bar.
• Phone view — the zoom view laid out for a phone held upright: a thumb-reachable vertical slider on the right edge, step buttons, and pinch-to-zoom on the image.
• Vertical 3D view — a vertical scale bar; moving it slides the current image/metadata away in depth (bursting toward the viewer or sinking into the screen) while the next one arrives.

Data

• data.json — one entry per dataset: SSBD ID, dataset name, title, license, contact, physical crop length (µm), pixel dimensions, and thumbnail filename.
• thumbnails/ — a square, center-cropped PNG thumbnail per dataset, rendered from the lowest usable resolution level of each dataset's OME-Zarr array (composited from active channels using their omero color/window metadata).

The physical scale used to rank datasets comes from the SSBD metadata REST APIs (v1, v2, v3) — specifically each dataset's X/Y scale (µm/pixel). Datasets the API has no scale metadata for are excluded rather than falling back to a less-authoritative estimate.

Each dataset's license (as recorded in the SSBD:database) is shown on its card; check it before reusing an image.

Regenerating the data

scripts/ holds the pipeline used to build data.json and thumbnails/ from the openssbd/ssbd-bff CSV listing:

1. ssbd_omezarr_area.py — lists OME-Zarr datasets from a bff CSV export by physical image area (fetches each dataset's .zattrs for pixel size).
2. generate_thumbnails.py — renders and center-crops one square thumbnail per SSBD project from its OME-Zarr array.
3. fetch_ssbd_api_scale.py — looks up each dataset's X/Y/Z/T scale from the SSBD v1/v2/v3 REST APIs.
4. merge_api_scale.py — recomputes the physical crop length using the API-sourced pixel size.

These require zarr, fsspec, numpy, and Pillow, and network access to dmss3gw.riken.jp and ssbd.riken.jp.

Running locally

This is a static site — any static file server works, e.g.:

python3 -m http.server 8000

then open http://localhost:8000/.