BBMRI-NL Population Imaging Platform

Summary BBMRI-Imaging
With the population imaging platform, users can easily run image-analysis pipelines on medical images. The medical images can be stored in a central XNAT database. Then, users can query data and available pipelines, select pipelines for processing and inspect intermediate and final results.

What is BBMRI-Imaging?
The population imaging platform is a service that facilitates the running of medical image-analysis pipelines on medical images. It provides the user with an XNAT database for storing images, an easy-to-use platform to run pipelines on these images to calculate imaging biomarkers, and a viewer to inspect intermediate and final results. The tools used for processing are provided under an open-source license (Apache 2.0). The following tools are provided:

  • Fastr (http://fastr.readthedocs.io): Pipeline engine and processing manager. This tool is developed by the Erasmus MC in BBMRI WP3 and WP5.
  • PIM (https://gitlab.com/bbmri/pim): Web framework for online Pipeline Inspection and Monitoring. Exposes a REST API for being inter operable with pipeline engines. Fastr supports visualizing the pipelines and their progress in PIM. This tool is developed by LUMC in BBMRI WP3.
  • StrongR (https://gitlab.com/bbmri/infra/strongr): StrongR is a novel way for enabling elastic scaling of batch processing in the cloud, allowing pipeline frameworks to exploit the benefits of cloud computing. Unlike traditional cloud-based setups, where one would deploy a static, temporary cluster, StrongR allows you to be truly elastic: it will create worker nodes when processing power is required, and shut them down when not enough work is available. In this case, cloud resources are only allocated when they are really used. Furthermore, it allows the upscaling of the processing whenever there is more demand for computational power. Finally, StrongR can interface with multiple cloud providers, allowing users to do processing in the cloud of their choice. StrongR is developed by Erasmus MC in BBMRI WP3.

 

The following illustration gives an overview of the interaction between the different components in the IT infrastruct built for BBMRI Imaging.

 

Why BBMRI-Imaging?
The population imaging platform facilitates the calculation of imaging biomarkers for researchers. The platform is easy to use, also for people without a technical background. The provided image-analysis pipelines are established methods that have proven their performance on large datasets.

Who should use BBMRI-Imaging?
The platform is developed for researchers that would like to extract imaging biomarkers. 

Status of BBMRI-Imaging?
Currently, images can be stored in the TraIT XNAT (www.ctmm-trait.nl/trait-tools/xnat, https://xnat.bmia.nl).

So far, eight pipelines have been implemented:

  • Population based statistical analysis of brain structures (LUMC)
  • Whole brain segmentation (EMC)
  • Tissue segmentation (EMC)
  • Hippocampus segmentation (EMC)
  • White-matter-lesion segmentation (EMC)
  • Brain-structure segmentation (EMC)
  • Epi-cardial-fat segmentation (EMC)
  • Connectome reconstruction (UMCU)

 

How to start using BBMRI-Imaging?
Contact one of the WP leaders.

Training information for BBMRI-Imaging?

Support for BBMRI-Imaging?

Link to BBMRI-Imaging?
www.populationimaging.eu

References and other links for BBMRI-Imaging?
www.populationimaging.eu

For more information on BBMRI-Imaging contact:
BBMRI-NL’s Population Imaging Platform leader: Annegreet van Opbroek: a.vanopbroek@erasmusmc.nl , Marcel Koek: m.koek@erasmusmc.nl  or the Service Desk

BBMRI-NL’s WP leader: Aad van der Lugt: a.vanderlugt@erasmusmc.nl, Wiro Niessen: w.niessen@erasmusmc.nl, Hilleke Hulshoff Pol: h.e.hulshoff@umcutrecht.nl