Launch ndea

Open one dataset

Pass an AnnData or supported MuData Zarr store to view:

ndea view path/to/data.zarr

The view subcommand is optional, so this is equivalent:

ndea path/to/data.zarr

ndea starts the local server on http://localhost:5055 and asks the operating system to open its default browser. The interface requires Chrome or Edge. If another browser opens, copy the printed URL into Chrome or Edge. Use --no-open to open the URL yourself.

Open several datasets

Pass several Zarr paths when they do not need image linkage or per-dataset channel settings:

ndea view experiment-a.zarr experiment-b.zarr

Use a YAML project when you need stable dataset names, mounted OME-Zarr plates, channel display settings, or a shared observation-column selection:

ndea view project.yaml

See Project YAML for both accepted dataset syntaxes.

Limit loaded observation columns

Large obs tables take longer to ingest. Keep only columns needed for filtering, colouring, annotation, and image linkage:

ndea view data.zarr --obs-columns cell_type,treatment,fov_name,t,x,y

Spatial columns required for image linkage are added automatically when detected.

Confirm the session

A successful launch prints the number of loaded observations, variables, and embeddings, then the application URL. In the browser:

1. confirm that the Scatter view lists the expected embedding;
2. colour the scatter by an observation column;
3. select points and confirm that linked table counts change;
4. if a plate is mounted, focus a row and confirm that the Image Viewer loads its field of view.

If a dataset opens but a particular view is empty, check Supported formats and Troubleshooting before changing the source data.