Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/danburonline/neuromorphovis-service
https://github.com/danburonline/neuromorphovis-service
Last synced: about 1 month ago
JSON representation
- Host: GitHub
- URL: https://github.com/danburonline/neuromorphovis-service
- Owner: danburonline
- Created: 2024-03-06T12:54:06.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2024-04-18T17:04:17.000Z (8 months ago)
- Last Synced: 2024-04-19T17:35:01.226Z (8 months ago)
- Language: Python
- Size: 54.7 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# NeuroMorphoVis as a Service
This repository contains a proof of concept for a Python web server to run the open-source [NeuroMorphoVis](https://github.com/BlueBrain/NeuroMorphoVis) tool as a cloud service. It allows for physics-based reconstructions of neuronal soma cells and other morphological processes for analysis and simulations.
## Quick Start
### Prerequisites
1. VS Code with the [Dev Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers) extension installed
2. Docker installed and running on your machine
3. Make sure you are connected to the EPFL VPN to download specific packages required for NeuroMorphoVis.
### Setup the Dev Container
1. Open the repository in VS Code
2. Click on the right bottom corner button and press `Reopen in Container`
3. Wait for the Dev Container to build and start, this can take a few minutes if it's the first time
## Run the NeuroMorphoVis Service
1. Build the Docker container: `docker build -t neuromorphovis .`
2. Run the Docker container: `docker run -p 8000:8000 neuromorphovis`
3. Access the web server at `http://localhost:8000/health`
4. CD into the Docker container and run CLI scripts or access the API via `http://localhost:8000`
### Example CLI Script
```bash
python neuromorphovis.py --blender=blender/bbp-blender-3.5/blender-bbp/blender --input=file --morphology-file=docs/example/example-file.swc --export-soma-mesh-blend --export-soma-mesh-obj --output-directory=$(pwd)/output
```
## ⚠️ Quick Fixes
- Currently there is a bug in the NeuroMorphoVis addon related to the topology re-tesselation as reported [here](https://github.com/BlueBrain/NeuroMorphoVis/issues/208). Due to this the CLI command `--export-soma-mesh-obj` will not work as expected. To fix this, you need to manually comment out the following lines in the `neuromorphovis.py` script:
```python
self.mesh.topology_tessellation = nmv.enums.Meshing.TopologyTessellation.get_enum(
arguments.topology_tessellation)
```
Afterwards, this quick fix will allow you to export the soma mesh as an OBJ file.
## How to Work with the API
When you start the Docker container a FastAPI web server will boot up and be available under `http://localhost:8000`. You'll find Hoppscotch API requests inside the [`docs`](/docs/api/api-specs.json) directory as a JSON that you can import into the [Hoppscotch](https://hoppscotch.io) app. This will allow you to interact with the API and run the CLI scripts from the web interface.
There are also [example morphology files](/docs/example/example-file.swc) that you can try out with the API.