unravel.image_io.tif_to_tifs module#

Use io_tif_to_tifs from UNRAVEL to load a 3D .tif image and save it as tifs.

Input:

image.tif (either from -i path/image.tif or largest *.tif in cwd)

Outputs:

./<tif_dir_out>/slice_`*`.tif series
./parameters/metadata (text file)

Next command:

reg_prep to prep autofluo images registration

Usage:#

io_tif_to_tifs -i <path/image.tif> -t 488 [-v]

unravel.image_io.tif_to_tifs.parse_args()[source]#

unravel.image_io.tif_to_tifs.find_largest_tif_file()[source]#: Find and return the path to the largest .tif file in the current directory

unravel.image_io.tif_to_tifs.load_3D_tif(tif_path, desired_axis_order='xyz', return_res=False)[source]#: Load full res image from a 3D .tif and return ndarray Default: axis_order=xyz (other option: axis_order=”zyx”) Default: returns: ndarray If return_res=True returns: ndarray, xy_res, z_res (resolution in um)

unravel.image_io.tif_to_tifs.metadata_from_3D_tif(tif_path)[source]#: Returns tuple with xy_voxel_size and z_voxel_size in microns from a 3D .tif

unravel.image_io.tif_to_tifs.save_as_tifs(ndarray, tif_dir_out, ndarray_axis_order='xyz')[source]#: Save <ndarray> as tifs in <Path(tif_dir_out)>

unravel.image_io.tif_to_tifs.main()[source]#