# Running Pipelines in MagellanMapper

## Vignette

See our [vignette](https://github.com/sanderslab/magellanmapper/blob/master/bin/sample_cmds_bash.ipynb) for examples on using MM.

## Start a processing pipeline

**Note**: This pipeline script is deprecated. See our vignette above for running similar pipelines.

Automated processing will attempt to scale based on your system resources but may require some manual intervention. This pipeline has been tested on a Macbook Pro laptop and AWS EC2 Linux (RHEL and Amazon Linux based) instances.

Optional dependencies:

- ImageJ/Fiji with the BigStitcher plugin: required for tile stitching; downloaded automatically onto a server when running `deploy.sh`
- ImageMagick: required for exporting a stack of planes to an animated GIF file
- FFMpeg: required to export a stack to a movie format such as MP4
- [Slack incoming webhook](https://api.slack.com/incoming-webhooks): to notify when tile stitching alignment is ready for verification and pipeline has completed

### Local
Run a pipeline in `pipelines.sh`.

For example, load a `.czi` file and display in the GUI, which will import the file into a Numpy format for faster future loading:

```
bin/pipelines.sh -i data/HugeImage.czi
```

To sitch a multi-tile image and perform cell detection on the entire image, which will load BigStitcher in ImageJ/Fiji for tile stitching:

```
bin/pipelines.sh -i data/HugeImage.czi -p full
```

See `bin/pipelines.sh` for additional sample commands for common scenarios, such as cell detection on a small region of interest. The file can be edited directly to load the same image, for example.

### Server

You can launch a standard server, deploy MagellanMapper code, and run a pipeline. See [tools for AWS cloud management](cloud_aws.sh) for more details.