Image IO submodule

The image IO submodule provides various options to load and save image data. It supports common formats like tiff and nifti.

Installation

The image IO submodule 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.IO.image.load. For example, the general purpose load_any function which can load many common file formats:

from brainglobe_utils.IO.image import load
load.load_any('mydata.tif')

There are also functions specific to particular file formats:

from brainglobe_utils.IO.image 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')

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

Or to load a directory containing a series of 2D tiffs as a dask array:

from brainglobe_utils.IO.image.load import read_with_dask

signal_array = read_with_dask("/path/to/image_directory")

Saving images

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

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

There are also functions specific to particular file formats:

from brainglobe_utils.IO.image 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')

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