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Getting started

Installation

pip install brainhops

Description

brainhops is a python library to apply spatial transformations to images. It aims to support most image and transformation formats used in neuroimaging and in microscopy. Most importantly, it aims to scale to very large images. To this end, it supports multiple array backends (numpy, cupy, dask.array), which allows user to benefit from their acceleration and parallelization capabilities.

brainhops can be used through two different interfaces:

  • a command-line interface (brainhops --help), which exposes a subset of functionalities such as

    • applying chains of transformations to images, meshes or point clouds;
    • converting between different images and transformations formats.

  • a python API (import brainhops) that abstracts away many types of spatial transformations and interfaces with most neuroimaging and microscopy formats.