image_io

image_io provides various options to load and save image data. It supports common formats like tiff, nrrd and nifti.

Installation

image_io is provided as part of brainglobe_utils which comes with the one-line BrainGlobe install (pip install brainglobe). It will also be fetched by most of our tools if you decide to install them as standalone.

Loading images

All options to load images are provided under brainglobe_utils.image_io.load. For example, the general purpose load_any function which can load many common file formats:

from brainglobe_utils.image_io import load
load.load_any('mydata.tif')

There are also functions specific to particular file formats:

from brainglobe_utils.image_io import load

# tiff
load.load_img_stack('mydata.tif', x_scaling_factor=1, y_scaling_factor=1, z_scaling_factor=1)

# directory containing a sequence of 2D tiffs
load.load_from_folder('/path/to/dir')

# nrrd
load.load_nrrd('mydata.nrrd')

# nifti
load.load_nii('mydata.nii')

Saving images

All options to save images are provided under brainglobe_utils.image_io.save. For example, the general purpose save_any function which can save a numpy array to many common file formats:

from brainglobe_utils.image_io import save
save.save_any(my_array, 'mydata.tif')

There are also functions specific to particular file formats:

from brainglobe_utils.image_io import save

# tiff
save.to_tiff(my_array, 'mydata.tif')

# directory containing a sequence of 2D tiffs
save.to_tiffs(my_array, '/path/to/dir/prefix')

# nrrd
save.to_nrrd(my_array, 'mydata.nrrd')

# nifti
save.to_nii(my_array, 'mydata.nii')