img2omezarr converts microscopy image files to OME-Zarr. It has both a command line user interface and a GUI aimed to make it easy
for regular users to upload their data to OME-Zarr.
Testing needed; work in progress
cargo build -p img2omezarr --features cli --bin img2omezarrPerformance benchmarks are documented in docs/benchmarks.md.
NGFF version support is documented in docs/ngff-support.md. The real-world fixture matrix is tracked in docs/validation.md.
img2omezarr convert INPUT OUTPUT.ome.zarr
img2omezarr batch --output-dir OUT INPUT...Run img2omezarr --help for the full CLI options.
The GUI can save S3 profiles between runs. Profile metadata is written to the
platform config directory. Access keys are stored separately in
credentials.toml in the same app config directory, not in the main settings
file.
Build the GUI with S3 support:
cargo run -p img2omezarr-gui --features upload-s3Select s3 as the upload target, enter a profile name, bucket, prefix, region,
endpoint, and credentials, then press Save.
General GUI settings are persisted between runs. S3 profile metadata is stored with those settings, but access keys are written only to the separate credentials file. On Unix, the GUI writes that file with owner read/write permissions.
This code is under MIT. But note that some libraries it depends on are GPL.