Atlas Alignment

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Atlas Alignment is a toolbox to perform multimodal image registration. It
includes both traditional and supervised deep learning models.

This project originated from the Blue Brain Project efforts on aligning mouse
brain atlases obtained with ISH gene expression and Nissl stains.

Official documentation

All details related to installation and logic are described in the
official documentation.

Installation

Installation Requirements

Some of the functionalities of atlalign depend on the TensorFlow implementation
of the Learned Perceptual Image Patch Similarity (LPIPS). Unfortunately, the
package is not available on PyPI and must be installed manually as follows
for full functionality.
```shell script
pip install git+http://github.com/alexlee-gk/lpips-tensorflow.git#egg=lpips_tf


You can now move on to installing the actual `atlalign` package!
#### Installation from PyPI
The `atlalign` package can be easily installed from PyPI.
```shell script
pip install atlalign

Installation from source

As an alternative to installing from PyPI, if you want to try the latest version
you can also install from source.
```shell script
pip install git+https://github.com/BlueBrain/atlas_alignment#egg=atlalign


#### Installation for development
If you want a dev install, you should install the latest version from source with
all the extra requirements for running test and generating docs. 
```shell script
git clone https://github.com/BlueBrain/atlas_alignment
cd atlas_alignment
pip install -e .[dev,docs]

Examples

You can find multiple examples in the documentation. Specifically, make
sure to read the
Building Blocks
section of the docs to understand the basics.

Data

You can find example data on Zenodo.
Unzip the files to ~/.atlalign/ folder so that you can use the data.py module
without manual specification of paths.

Allen Brain Institute Database

You can find and download ISH data from Allen Brain Institute thanks to
Atlas Download Tools repository.

Funding & Acknowledgment

This project was supported by funding to the Blue Brain
Project, a research center of the Ecole polytechnique fédérale de Lausanne, from
the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.