Children's Research Integration System: ChRIS


Rudolph Pienaar, PhD
Technical Director
Fetal-Neonatal Neuroimaging and Developmental Science Center

Staff Scientist
Boston Children's Hospital

Instructor in Radiology
Harvard Medical School



overview of talk

traditional slides...

live interaction

ancilliary projects


overview of talk

ChRIS is:

  • [Boston's] " Children's Research Informatics System"
  • a web-based research/clinical workflow manager
  • and more...

overview of talk


unmet need

  • why aren't research informatics tools in more widespread clinical use?
  • why is real time collaboration/sharing on medical data so 1990s?

value proposition

  • bridge research/clinical gap using web 2.0 metaphors
  • track, share, process, collaborate

ChRIS overview

live demo


unmet need...


  • collect and manage medical data with seamless integration with hospital systems
  • process data
  • visualize and interact with data
  • share data
  • real time collaboration

The Children's Research Information System, ChRIS, is a simple and intuitive Software-as-a-Service platform that allows users to:


unmet need...


  • Image analysis requires advanced scientific computing expertise

making scientific computing more accessible to wider clinical and research communities

  • unix commands
  • disparate data and file systems
  • disjointed analytical tools and modules

unmet need...

  • lack of pipeline tools that combine processing modules, work flow integration, and a modern user interface
  • high barrier to entry by non-technical users

making scientific computing more accessible to wider clinical and research communities


value added proposition: research to clinical


Many existing, mature, analysis streams exist primarily in the research domain that can bring considerable value-added information to the clinical workflow

  • white matter tractography for surgical planning
  • automatic brain surface reconstrution
  • automatic brain volumetric segmentation
  • automatic tumor detection and measurement

the traditional approach to research pipelines...

what is typical domain knowledge for conducting numerical research?

  • specialized tools with high degree of domain knowledge
  • UNIX (Linux or Mac) command line
  • intimate knowledge of clusters and scheduling

use the web, Luke...

shifting to the web allows for:

  • more familiar interface metaphor
    • web 2.0 "social" interaction
    • posting/sharing
  • moves the burden of maintenance away from end user
  • allows for mobile

what is ChRIS?



ChRIS is a bio-medical data workflow manage that allows easy and intuitive collection, analysis, and sharing of data between parties.


what is ChRIS?

ChRIS also...

  • allows for advanced view rendering
  • allows for sharing of images
  • allows for immersive real time collaboration
  • allows for post-processing of images

components

  • collect
  • manage
  • analyze
  • view
  • collaborate

collect image data

  • seamlessly connect to standard PACS with Query/Retrieve
  • direct access to server filesystem
  • drag-n-drop from local client into server
  • ssh/scp underpinning for secure network transfers

collect image data


manage image data


  • all "data is stored in a time-based feed
  • feeds are basically file-browsers
  • feeds can be annotated with free form notes
  • shared feeds can support comments between parties

analyze image data


  • a "plugin" mechanism offers the ability to accept feed data and process data
  • ChRIS is usually configured to communicate transparently with an HPC
  • plugins are mostly non-interactive analysis pipelines
  • interactivity is available as a pre-processing step

analyze image data



view image data


  • image data in feed can be viewed directly in simple drop down window
  • image data can be viewed in more sophisticated fashion with specialized viewing modes
  • advanced sharing using 3rd party backends (Google Real Time API / Dropbox API)

real time collaboration


  • image data can be shared between collaborators
  • Google RealTime API
  • a realtime JSON object is shared and updates each viewer independently
  • (akin to multi-player games)
  • shared screen components (like cursor)

real time collaboration



real time demo...


  • ChRIS instance

real time demo...


  • ChRIS instance

Ancilliary projects


  • https://fnndsc.github.io/mi2b2

Development team


  • Jorge "To Be" Bernal, PhD
  • Nicolas "VJ" Rannou, MSc
  • Rudolph "Cat Herder" Pienaar, PhD
  • Daniel "X Slicer" Haehn, PhD
  • Daniel "Game On" Ginsburg, MSc
  • Ellen "Doc" Grant, MD

further references... 


  • https://github.com/FNNDSC/chrisreloaded
  • https://github.com/FNNDSC/ChRIS_API
  • https://github.com/FNNDSC/viewerjs
  • https://github.com/FNNDSC/mi2b2
  • https://github.com/FNNDSC/vjs
  • https://github.com/slicedrop
  • https://goxtk.com

thank you...