save_as

1. save_as#

mbo_utilities.save_as() is a convenience function for exporting common data formats processed from MBO datasets.

It can save ScanImage tiffs or ScanMultiROIReordered arrays into:

  • .tiff

  • .zarr

  • .h5

This function is usable from:

  • terminal (mbo assemble CLI)

  • Python script

  • Jupyter/IPython notebooks

save_as automatically handles large datasets, metadata, chunking, and scan phase correction.

It uses tifffile, h5py, and optionally zarr for efficient IO.

1.1. Terminal usage (CLI)#

# Quickly open file/folder, process, and save
assemble path/to/data/ --save path/to/output/ --zarr

# Optional arguments:
# --trimx, --trimy for trimming
# --target_chunk_mb for chunk size
# --summary to include per-plane statistics

When no --save path is given, only metadata is printed.

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