unravel.image_io.metadata module#

Use io_metadata (m) from UNRAVEL to save x/y and z voxel sizes in microns as well as image dimensions to a metadata file in each sample directory.

Inputs:

  • .czi, .nii.gz, .h5, or TIF series (path should be relative to ./sample??)

Outputs:

  • ./parameters/metadata.txt (path should be relative to ./sample??)

Note

  • If -d is not provided, the current directory is used to search for sample?? dirs to process.

  • If the current dir is a sample?? dir, it will be processed.

  • If -d is provided, the specified dirs and/or dirs containing sample?? dirs will be processed.

  • If -p is not provided, the default pattern for dirs to process is ‘sample??’.

  • To test out -d/-p, use the utils_get_samples command to see which sample?? dirs will be processed.

Next command:

  • reg_prep for prepping autofluo images for registration

Usage for when metadata is extractable:#

io_metadata -i rel_path/full_res_img [-m parameters/metadata.txt] [-d space-separated list of paths] [-p pattern] [-v]

Usage for when metadata is not extractable:#

io_metadata -i tif_dir -x 3.5232 -z 6 [-m parameters/metadata.txt] [-d space-separated list of paths] [-p pattern] [-v]

unravel.image_io.metadata.parse_args()[source]#
unravel.image_io.metadata.print_metadata(metadata_path)[source]#
unravel.image_io.metadata.get_dims_from_tifs(tifs_path)[source]#
unravel.image_io.metadata.main()[source]#