Install

Install, update, and remove ndea on macOS with Apple silicon, on Linux, or on Windows.

Install the latest stable release

curl -fsSL https://czbiohub-sf.github.io/nd-embedding-atlas/install.sh | sh

The installer:

supports macOS on Apple silicon and Linux on x64 or arm64;
downloads the matching release binary and SHA-256 file;
verifies the checksum;
stores the binary under ~/.ndea/versions/<tag>/ndea; and
points ~/.local/bin/ndea at that version.

Ensure ~/.local/bin is on PATH, then check the installation:

ndea --version
ndea doctor

Select a version or channel

Pass a release tag or a channel name as an argument:

# A specific tag
curl -fsSL https://czbiohub-sf.github.io/nd-embedding-atlas/install.sh | sh -s -- v0.1.0

# The active alpha, beta, or release candidate
curl -fsSL https://czbiohub-sf.github.io/nd-embedding-atlas/install.sh | sh -s -- pre-release

The accepted values are stable (the default), latest, pre-release, and any release tag.

Install with mise

mise can manage ndea alongside your other tools:

mise use -g github:czbiohub-sf/nd-embedding-atlas

mise downloads the same release binary and verifies its checksum. Versions are given without the leading v, as in @0.1.0.

ndea update detects a mise-managed binary and updates the active mise config through mise. It does not create a competing ~/.ndea/versions installation. Channels work the same way, including ndea update --channel pre-release.

Select a known mise version explicitly when needed:

mise use -g --pin github:czbiohub-sf/nd-embedding-atlas@0.1.0

Update or change versions

ndea update
ndea update --channel pre-release

For standalone installs, updates verify the checksum, atomically replace the active symlink, and keep only the active version by default. ndea gc manages any inactive versions retained with ndea update --no-gc.

To install a specific older standalone release, remove the current standalone installation before running the installer with an explicit tag:

rm -f "$HOME/.local/bin/ndea"
rm -rf "$HOME/.ndea"
curl -fsSL https://czbiohub-sf.github.io/nd-embedding-atlas/install.sh | sh -s -- v0.1.0

For mise installs, ndea update updates the active mise config through mise. Select a specific version with mise use -g --pin github:czbiohub-sf/nd-embedding-atlas@0.1.0. A running ndea view process continues using the version it started with in either layout.

On Windows, re-run the installer with the tag you want; no removal step is needed.

Remove ndea

Remove the active symlink, installed versions, and extracted native-library cache:

rm -f "$HOME/.local/bin/ndea"
rm -rf "$HOME/.ndea" "${XDG_CACHE_HOME:-$HOME/.cache}/ndea"

This does not remove source datasets.

See the CLI reference for every maintenance command.