Requirements

Runtime

nd-embedding-atlas runs as a local server and opens its interface in a browser. The release installer supports:

• macOS on Apple silicon (arm64)
• Linux on x86_64
• Linux on arm64
• Windows on x86_64

Windows on arm64 runs the x86_64 binary under emulation; there is no native arm64 build. Windows installs are managed by re-running the installer, because ndea update is available only on macOS and Linux.

Browser and graphics

Use a current Chrome or Edge release with WebGPU enabled. The scatter renderer requires WebGPU; Firefox is not supported because it does not provide the required WebGPU implementation by default.

Run ndea doctor to check the installed binary, active symlink, and installed versions. On Windows there is no symlink to report: the installer writes a single ndea.exe. On a remote Linux workstation or HPC system, follow WebGPU on HPC to establish a secure browser origin and enable the Vulkan backend.

Data access

The server process must be able to read every AnnData, MuData, and OME-Zarr path supplied at launch. Paths in a project YAML file are resolved relative to that file.

Plan for additional working storage under ~/.ndea/:

• installed versions live under ~/.ndea/versions/;
• updates retain only the active version by default;
• native DuckDB extraction and local caches use ~/.cache/ndea/.

On Windows the equivalent paths are %LOCALAPPDATA%\ndea\bin\ndea.exe for the binary and %LOCALAPPDATA%\ndea\<version>\ for the DuckDB cache.

The application reads local Zarr stores directly. Large imaging datasets should remain on low-latency local or shared storage; storage latency and chunk layout directly affect crop loading.