Running Pipelines in MagellanMapper

Vignette

See our vignette 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: 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 for more details.