https://github.com/bluebrain/bbp-atlas-web-exporter

Export the Blue Brain Atlas Pipeline to be consumed by the Atlas web app
https://github.com/bluebrain/bbp-atlas-web-exporter

atlas database

Last synced: 5 months ago
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Export the Blue Brain Atlas Pipeline to be consumed by the Atlas web app

• Host: GitHub
• URL: https://github.com/bluebrain/bbp-atlas-web-exporter
• Owner: BlueBrain
• License: apache-2.0
• Created: 2024-09-03T12:36:06.000Z (almost 2 years ago)
• Default Branch: master
• Last Pushed: 2024-11-14T10:25:29.000Z (over 1 year ago)
• Last Synced: 2025-10-27T14:14:19.871Z (8 months ago)
• Topics: atlas, database
• Language: C
• Homepage:
• Size: 52.8 MB
• Stars: 1
• Watchers: 4
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: readme.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE.txt
  • Authors: AUTHORS.txt

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README

          
# BlueBrainAtlas WebExporter

The web exporter is a suite of tools to facilitate the conversion and export of the Blue Brain Atlas pipeline to web-friendly datasets to be consumed by the Atlas web app.  

Once installed, this package exposes two CLIs:

- `cellexport`

- `parcellationexport`

# Installation

`pip install "blue-brain-atlas-web-exporter"`

This will automatically install the CLIs listed below and make them available in your `PATH`.

# Examples

## cellexport

The CLI `cellexport` converts a cell-position SONATA file into a set of RandomAccessBuffer files (RAB) as well as a JSON metadata file containing a few computed metrics.  

Here is the list of arguments:

- `--help` displays the help menu

- `--version` displays the version number

- `--hierarchy ` input path to the brain region hierarchy file (commonly called *1.json*) — **mandatory**

- `--sonata ` input path to the SONATA file containing cell positions/orientation/brain-regions/celltypes — **mandatory**

- `--downsampling-factor ` factor to downsample the data — **optional** (default: `1`, no downsampling. Example: a factor of 100 will keep only one value every 100)

- `--out-postion ` output path to the RAB file that contains the cell positions — **mandatory**

- `--out-cell-type ` output path to the RAB file that contains the cell types — **mandatory**

- `--out-orientation ` output path to the RAB file that contains the cell orientations — **mandatory**

- `--out-region ` output path to the RAB file that contains the cell region IDs — **mandatory**

- `--out-metadata ` output path the JSON file that contains the metadata — **mandatory**

## parcellationexport

The CLI `parcellationexport` computes all the meshes (`.OBJ` files) as well as the binary masks (`.nrrd` files) for all the regions available in both the hierarchy file (input) and the annotation volume (input). Many intermediate regions from the hierarchy file do not have any voxel representation and instead are composed of voxels from their child region, thus, this CLI computes all the aggregations necessary to recreate binary masks for those regions. This CLI also output a JSON metadata file with metrics regarding the volume and volume ration for all the regions.  

For each region, this CLI also generates a list of neighbour regions (`adjacentTo`) and the list of neighbour region that are on the same layer, when applicable (`continuousWith`). Note that `continuousWith` is a subset of `adjacentTo` and while `adjacentTo` entirely relies on volumetric data, `continuousWith` leverages the region hierarchy and in particular the regions' acronyms. Those metadata are part of the main JSON payload, alongside with the region volumes.

Here is the list of arguments:  

- `--help` displays the help menu

- `--version` displays the version number

- `--hierarchy ` input path to the brain region hierarchy file (commonly called *1.json*) — **mandatory**

- `--parcellation-volume ` input path to the parcellation file format (*.nrrd*) — **mandatory**

- `--out-mesh-dir ` output path for the directory where the region/parcellation mesh files (*.obj*) will be written. Each file will have the name corresponding to the ID of the region (example: `997.obj` for the whole brain) — **mandatory**

- `--out-mask-dir ` output path for the directory where the region/parcellation binary mask volumes (*.nrrd*). Each file will have the name corresponding to the ID of the region (example: `997.nrrd` for the whole brain) — **mandatory**

- `--out-metadata ` output path to the JSON file that contains the metadata - **mandatory**

# 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 © 2015-2022 Blue Brain Project/EPFL