BatchConvert

Perform parallelised conversion of image data collections to OME-Zarr using BatchConvert

Important note: BatchConvert is currently only supported on unix-based systems

As input, use the tiff_series dataset.

Unary conversion

batchconvert omezarr \
/path/to/tiff_series \
/path/to/output_dir 

This command maps each input file in the tiff_series folder to a single OME-Zarr, which is then transferred to the output_dir folder.

Check the content of the output_dir folder:

ls /path/to/output_dir

Optional: Inspect the created OME-Zarr.

Aggregative conversion

batchconvert omezarr \
--merge_files \
/path/to/tiff_series \
/path/to/concatenated_output_dir

This conversion mode assumes that the input files are part of the same image and thus will merge them along a specific axis during the conversion process. The --merge_files flag specifies the grouped conversion option.

Check the content of the output_dir folder:

ls /path/to/concatenated_output_dir

Optional: Inspect the created OME-Zarr.

Aggregative conversion with specific chunking, downscaling and compression parameters

batchconvert omezarr \
--merge_files \
--compression_zarr zlib \
-ms 32 \
-cx 32 \
-cy 32 \
-cz 6 \
/path/to/tiff_series \
/path/to/concatenated_rechunked_output_dir

Here we do not only concatenate images, but we create a resolution pyramid and specify chunk sizes in x, y and z dimensions.

Check the content of the zarr_series_concatenated_rechunked folder:

ls /path/to/concatenated_rechunked_output_dir

Optional: Inspect the created OME-Zarr. Compare it to the one created earlier.