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Convert TIFF to OME-Zarr

Note

There is also a CLI command for conversion. See the CLI Reference or run iohub convert --help.

TIFFConverter

Convert Micro-Manager TIFF formats (OME-TIFF, ND-TIFF) into HCS OME-Zarr. Each FOV will be written to a separate well in the plate layout.

Parameters:

Name Type Description Default
input_dir str | Path

Input directory path

 required
output_dir str | Path

Output zarr directory path

 required
grid_layout bool

Whether to lay out the positions in a grid-like format based on how the data was acquired (useful for tiled acquisitions), by default False

 False
chunks tuple[int] or Literal['XY', 'XYZ']

Chunk size of the output Zarr arrays, by default None (chunk by XYZ volumes or 500 MB size limit, whichever is smaller)

 None
hcs_plate bool

Create NGFF HCS layout based on position names from the HCS Site Generator in Micro-Manager (only available for OME-TIFF), and is ignored for other formats, by default None (attempt to apply to OME-TIFF datasets, disable this with False)

 None
version Literal['0.4', '0.5']

OME-NGFF version for the output Zarr store, by default "0.4". Version "0.4" uses Zarr v2 format, version "0.5" uses Zarr v3 format.

 '0.4'
Notes

The image plane metadata for each FOV is aggregated into a JSON file, and placed under the Zarr array directory (e.g. /row/column/fov/0/image_plane_metadata.json).

__call__()

Runs the conversion.

Examples:

>>> from iohub.convert import TIFFConverter
>>> converter = TIFFConverter("input/path/", "output/path/")
>>> converter()