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
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
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
ChRIS-45MinuteTalk
By Rudolph Pienaar
ChRIS-45MinuteTalk
A general overview of ChRIS... shortcomings in conventional approaches, live demo, video, mi2b2.
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