Voxio: I/O package for 3D images

Usage

• Read images in parallel with simple_read_images(image_paths); convenience function with finder simple_find_read_images(image_directory, image_format)
• Read volumes that would require more than system memory in chunks, use reader to perform compute/analysis chunk_read_stack_images(image_paths, image_reader)
• Remove artifacts from volume with single object clear_everything_but_largest_object(image_paths, output_directory)
• Alternative to scipy.ndimage.label for situations with insufficient memory label_binary_image(image_paths, output_directory)
• Interpolate along the first dimension (z-axis) morphological_interpolation_max_resolution_spacing(labeled_stack, ceiled_inter_stack_voxel_distance)

Installation

pip install voxio