BioImage Model Zoo

The Models tab lists the models of the BioImage Model Zoo beside cellmap’s Hugging Face models, and runs the ones you tick as type: bioimage models. Their servers run in pixi.toml’s bioimageio environment, the type’s default (see Running a model in its own environment).

In the dashboard

Open the Models tab and expand BioImage Model Zoo. The list is read from bioimage.io’s artifact server (hypha.aicell.io) the first time and cached in ~/.cellmap_flow/bioimage/; Refresh reads it again, and so does the page by itself once the cached list is an hour old, and every hour while it is open. Its listing holds each model’s description, so 2D or 3D comes from the model’s input axes. When the server cannot be reached the legacy collection.json index is read instead, which lists fewer models.
Narrow it with the search box (name, description and tags), EM only (on by default: models whose tags, name or description say electron microscopy) and 2D / 3D. The arrow beside a model opens its page on bioimage.io; hovering over its name shows the full description.
Tick a model and check its Voxel (nm): z,y,x or one number for all three, the voxel size the model reads the data at. For the zoo’s EM models it is filled in with the one the model was trained at, and the line below says on what data and where that number comes from (hover for the source). No zoo model says it in its description, so cellmap-flow keeps them in cellmap_flow/models/bioimage_voxel_sizes.yaml, looked up by hand. Some were trained on downsampled data (the Platynereis nuclei model at 100x80x80 nm, z,y,x), and a few across several resolutions, for which you enter one. Other models need one entered.
Click Submit Models. As for the other models, unticking one and submitting again stops it, and a running one is ticked when the page is reloaded.

A ticked model is entered as its nickname (kind-seashell), and its layer and job are named after it (kind_seashell).

In a YAML file

The same model, without the dashboard:

models:
  mito:
    type: bioimage
    model: kind-seashell
    # voxel_size: [8, 8, 8]   # without it, the one it was trained at: 30x8x8 (MitoEM)

As in the dashboard, a zoo EM model reads at the voxel size it was trained at unless voxel_size says otherwise; any other model needs it. example/bioimage_em.yaml is a complete one.

From Python

from cellmap_flow.models.bioimage_catalog import list_bioimage_models, refresh_bioimage_models

for model in list_bioimage_models()["models"]:
    if model["em"]:
        print(model["key"], model["dims"], model["name"])

Each model has id (its alias on the server; in the legacy index a Zenodo DOI for older models), nickname, key (what it is loaded by), name, description, tags, dims ("2d", "3d" or None), em, weight_formats, license, cover, url (its bioimage.io page), trained (its row of bioimage_voxel_sizes.yaml, or None: voxel_size, trained_on, confidence, source, note) and, from the server, declared_voxel_size (nm, or None when its axes carry no unit: none of the zoo’s models declared one in October 2026, so a blank voxel size is refused at Submit unless trained gives one). refresh_bioimage_models() fetches the list again; a failed fetch raises ZooIndexError and keeps the cache.