Fiji - Arnheim

Disclaimer

This is alpha software. Versioning is errounous. Breaking changes happening on a daily basis. If you want to test the Arnheim platform please contact the developers directly.

Idea

Fiji-Arnheim provides a simple interface to start Fiji and connect it to a local Arnheim Instance. Fiji register itself as a worker and provides implementations to common image analysis tasks. ImageJ-1 Macros are supported to wrap and are registered as templates for the Tasks. (For detailed information on how Arnheim thinks about tasks and templates please visit the Arnheim documentation)

Prerequisites and Install

Fiji Arnheim heavily relies on PyImageJ for interfacing with ImageJ/Fiji. PyImageJ itself has various dependencies on Java and Maven. You can install PyImageJ via conda and then install Fiji Arnheim on top.

conda create -n fijiarnheim pyimagej openjdk=8
conda activate fijiarnheim
pip install fiji-arnheim

This install pyimagej together with maven. PyImageJ is then taking care of setting up a local instance of Fiji.

Usage

In order to run fiji-arnheim, activate your environment and run

fiji-arnheim

This will open Fiji with its UI (Usage is standard Fiji) and register it as a worker. You can call its implementations now from anywhere

Use Cases

Please read the Arnheim documentation thoroughly to get an idea for the use-cases and limitations of the Arnheim platform. Use cases include:

1. Remote Image Analysis: Use data stored on your institute server and analyse it on your local machine, without downloading and storing your data.
2. Big Data: Stream big datasets to your local machine (Napari required)
3. Combined Analysis Flows: Use Deeplearning in the Cloud, Cluster analysis, Web apps and Clients like ImageJ and Napari all in one analysis flow with metadata storage.
4. End-to-End Pipelines: Acquire Images on your Microscope, process them on the fly and get notified about results.

Please contact the developer for better explainations.

Testing and Documentation

So far Arnheim Fiji does only provide limitedunit-tests and is in desperate need of documentation, please beware that you are using an Alpha-Version

Build with

• Arnheim
• Bergen
• Grunnlag
• PyImage

Roadmap

This is considered pre-Alpha so pretty much everything is still on the roadmap

Deployment

Contact the Developer before you plan to deploy this App, it is NOT ready for public release

Versioning

There is not yet a working versioning profile in place, consider non-stable for every release

Authors

• **Johannes Roos ** - Initial work - jhnnsrs

See also the list of contributors who participated in this project.

License

Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)

Acknowledgments

• EVERY single open-source project this library used (the list is too extensive so far)