Search, download, and prepare atlas data.

Among different sources of data, Allen Brain Institute hosts a rich database of gene expression images, Nissl volumes, and annotation atlases. The Atlas-Download-Tools library can help you to download single section images and entire datasets, as well as the corresponding metadata. It can further pre-process the image data to place it in the standard reference space.

• Installation
  • Installation from PyPI
  • Installation from source
  • Installation for development
• How to use the package
  • Using the CLI
  • Using the python API
• Funding & Acknowledgment

Installation

Installation from PyPI

The atldld package can be easily installed from PyPI.

shell script pip install atldld

Installation from source

If you want to try the latest version, you can install from source. shell script pip install git+https://github.com/BlueBrain/Atlas-Download-Tools

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. shell script git clone https://github.com/BlueBrain/Atlas-Download-Tools cd Atlas-Download-Tools pip install -e '.[dev]'

How to use the package

Atlas-Download-Tools can be used through a command line interface (CLI), as well as programmatically through a python API.

At present the CLI is rather limited, but we are working on adding the most useful functionality as soon as possible.

Using the CLI

All functionality can be accessed through the atldld command and its sub-commands. For example: ```bash $ atldld

Information about the version of atldld

$ atldld info version $ atldld info version --help

Information about the cache folder

$ atldld info cache ```

One can also get dataset information through the CLI. bash $ atldld dataset info $DATASET_ID $ atldld dataset preview $DATASET_ID

To download a dataset use the atldld download command. shell $ atldld download dataset $DATASET_ID

For further information please refer to the help part of the corresponding command.

Using the python API

The package atldld has several functionalities to download data from Allen Brain Institute:

• One can find dataset IDs from a gene expression name: python from atldld.utils import get_experiment_list_from_gene dataset_ids = get_experiment_list_from_gene("Pvalb", axis='sagittal')

• One can download any dataset from a dataset ID: ```python from atldld.sync import DatasetDownloader downloader = DatasetDownloader(datasetid=DATASETID, **kwargs)

  One needs to fetch metadata before downloading a dataset.

  downloader.fetchmetadata() dataset = downloader.run() imageid, sectionnumber, img, imgexp, df = next(dataset) ``` Note that this functionality makes a simplifying assumption that the slices are perfectly parallel to one of the 3 axes.

• One can obtain metadata of a dataset: ```python from atldld.utils import CommonQueries, get_3d

  The axis {'sagittal', 'coronal'}

  axis = CommonQueries.getaxis(datasetid=DATASET_ID)

  The reference space

  refspace = CommonQueries.getreferencespace(datasetid=DATASET_ID)

  The 3d transformation of the dataset

  matrix3d = get3d(datasetid=DATASETID) ```

Funding & Acknowledgment

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

Copyright (c) 2021-2022 Blue Brain Project/EPFL