Children's Research Integration System: ChRIS


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

Staff Scientist
Boston Children's Hospital

Instuctor in Radiology
Harvard Medical School

overview of talk

traditional slides...

live interaction

ancilliary projects


overview of talk


  • unmet need
    • why aren't research tools more widely used clinically?
    • simple, intuitive, web-based interface
  • value proposition
    • traditional research pipeline analysis
    • shift to the web
  • ChRIS overview
  • live demo
  • use cases

unmet need...


The Children's Research and Integration System, ChRIS, is a simple and intuitive Software-as-a-Service (SaaS) platform that allows users to


  • collect and manage medical data with seamless integration to hospital systems
  • process data
  • visualize and interact with data
  • share both on- and off-line with real-time collaborative features

unmet need...


making scientific computing more accessible to wider clinical and research communities


  • Image analysis requires advanced scientific computing expertise
    • Unix commands
    • Disparate data and file systems
    • Disjointed analytical tools and modules

unmet need...


making scientific computing more accessible to wider clinical and research communities


  • Lack of pipeline tools that combine processing modules, work flow integration, and a modern user interface
  • Barrier to wider use by less technical users

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 clinical workflow

  • Automatic brain volumetric segmentation
  • Automatic tumor detection and measurement
  • White matter tractography for surgical planning
  • etc...

part of the schism...


Using these pipelines often requires

  • Linux/UNIX command line familiarity
  • Installing / maintaining / updating tools on local workstations
  • A considerable time investment to become fully familiar with the complexities of the tool usage



part of the schism...




Usage thus requires very specialised and skilled knowledge, and is self-limited usually to an ideosyncratic set of users.


the traditional approach to research pipelines...


what are typical methods for creating the previous analyses..?


  • UNIX (Linux or Mac) command line
  • Specialized tools with high degree of domain-knowledge
  • 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 manager that allows easy and intuitive collection, analysis, and sharing of any 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


  • Seamless and connection to standard PACS with Query/Retrieve
  • Direct access to server filesystem
  • Drag-and-drop from local client into server
  • Network based access via secure copy

manage image data


  • All "data" is stored in a time-based feed
  • Feeds are basically just file-browsers
  • Feeds can be annotated with freeform notes
  • Shared feeds can support comments between shared parties

analyze image data


  • A "plugin" mechanism offers the ability to accept feed data and process
  • ChRIS is usually configured to communicate transparently with an HPC
  • Plugins are mostly non-interactive analysis pipelines
  • Interactive plugins are also available -- these typically are used to pre-process data

view image data


  • Image data in feed can be viewed directly in simple drop down window
  • Image data can also be viewed in more sophisticated fashion with specialized viewing modes
  • Slice:Drop interaction

real time collaboration


  • Image view scene can be shared between ChRIS users
  • Once shared, all parties can interact on the same image viewer in real time.

real time demo...


  • ChRIS instance

Ancilliary projects


  • https://fnndsc.github.io/mi2b2

Development team


  • Jorge Bernal, PhD
  • Daniel Haehn, PhD
  • Daniel Ginsburg, MSc
  • Ellen Grant, MD
  • Nicolas Rannou, MSc
  • Rudolph Pienaar, PhD

thank you...



further references...


  • https://github.com/FNNDSC/chrisreloaded
  • https://github.com/slicedrop
  • http://goxtk.com