AI OnDemand (AIoD)

Overview

AI OnDemand (AIoD) is a framework developed by the Software Engineering & AI STP at the Francis Crick Institute that enables running any model on any compute environment without requiring user knowledge on how to install and run these models, let alone run them at scale on HPC/cloud compute (via Nextflow)!

It is designed to allow the use of arbitrary user interfaces (currently with a fully-fledged Napari plugin) to simplify usage and immediately visualise results while separating compute from visualisation.

Here's a simplified GIF outlining AIoD:

This documentation covers how to setup and use the framework, providing information for different user groups of AIoD:

• Wet lab scientists
• ML practitioners/experts
• HPC facility staff
• Future contributors!

Cricksters

Users within the Francis Crick Institute have automatic access to AIoD with no setup required.

If users outside of the Crick want to use AIoD on their HPC and are not HPC admins/specialists, please forward this page to your HPC admins. Alternatively, see our AIoD-Napari over SSH or Nextflow directly sections to use AIoD on your HPC without the need for OnDemand/virtual desktop.

Available Models

Although AIoD is a portable, efficient, expandable framework to run any model, for users the practical functionality is determined by which models are available!

Currently, the following models are integrated:

Cellpose StarDist Segment Anything (1+2) Empanada PlantSeg Etch-a-Cell Models

...with more on the way!

Contribution

AIoD is developed as an extendable platform, allowing users to easily add new models, preprocessing functions etc., that can become available to all or restricted users as desired. This simplifies and unifies running models on local, high-performance, or cloud compute!

If you want to use a model that is not currently available, see how to add a model or get in contact with us.

Repositories

• Segment-Flow — Nextflow pipeline that scalably, reproducibly distributes data over models
• Model Registry — Pydantic schema and model manifests for each model in AIoD
• AIoD Utils — Centralized I/O, custom RLE mask encoding, preprocessing functions...anything needed across front-ends and the Nextflow pipeline!
• Napari Plugin — Our plugin for Napari to make using the pipeline easier, with additional functionality for users!
• AIoD Documentation — This documentation!