ChRIS - A Service for Collecting, Organizing, Processing, and Sharing Medical Image Data in the Cloud

Rudolph Pienaar, PhD

Technical Director
Fetal-Neonatal Neuroimaging and Developmental Science Center

Staff Scientist
Boston Children's Hospital

introduction

Healthcare informatics is at an inflection point

This talk considers a particular perspective on the problem and proposes a solution

ChRIS

Research

Integration

Service

ChRIS

overview

Some trends confronting computing in healthcare and shaping the landscape

An introduction to our web-based system called ChRIS

Logical topology / design

UI considerations

Containerization

Healthcare informatics landscape

Clouds and untethered computing

Historical legacy

overview

healthcare informatics landscape...

Healthcare informatics is at an inflection point

This talk considers a particular perspective on the problem and proposes a solution

explosion of sensors

complex analytics

healthcare... philosophy shapes informatics

historically, healthcare is differential, not integrative

informatics is poorly understood and not seen necessarily as fundamental

classically information relationship is best described as 1:1

the practice of medicine is less integrative

healthcare "compute"...

provided by vendors with very specialized skills and market

thin, vertical stacks

silos...

Multiple, deep data sets exist in the healthcare dataverse

Largely disconnected and independent of each other

clinical

billing

health records

connections between data

data points, rich as they are, can be insufficient...

the more connections between points...

connections between data

the better!

some trends in informatics...

disparate, disconnected computing

the primacy of the browser as client platform

the rise of the ...

clouds and clouds and clouds...

what are "clouds"?

remember above all others that a "cloud" is really just...

someone else's computer

what do clouds do?

well... they rain...

essentially, we often think of "cloud" computing as less of "computing" and more as storage

we use "clouds" as hard drives in the sky

pull data (i.e. rain) and consume it locally

compute should be "free"...

If we abstract "clouds" to "containing" data...

then we can think of compute as being applied to data and somewhat independent of it

ChRIS...

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

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

many data sources... many compute sources...

via here

connect data here

to here...

and compute!

system topology

Main web server local data repository

remote compute nodes

data source (e.g. in hospital PACS)

distributed design...

web server

coordinator

data handler

compute handler

distributed design...

Red Hat collaboration

containerization

compute and io...

disparate, disconnected computing

data needs to be transferred from server host to remote location

data needs to be processed on remote location

local web server

data descriptor

data handler

pfurl --verb POST --raw --http 172.17.0.2:5055/api/v1/cmd --msg \
'{  "action": "pushPath",
    "meta": {
        "remote": {
            "key":         "someKey"
        },
        "local": {
            "path":         "/home/data"
        },
        "transport": {
            "mechanism":    "compress",
            "compress": {
                "encoding": "base64",
                "archive":  "zip",
                "unpack":   true,
                "cleanup":  true
            }
        }
    }
}' --quiet --jsonpprintindent 4

compute

local web server

exec descriptor

exec handler

compute

pfurl --verb POST --raw --http 172.17.0.2:5010/api/v1/cmd \
     --jsonwrapper 'payload' --msg \
'{  "action": "run",
        "meta": {
                "cmd":      "cal 7 1970",
                "auid":     "rudolphpienaar",
                "jid":      "cal-job-1234",
                "threaded": true
        }
}' --quiet --jsonpprintindent 4

compute... using a container

pfurl --verb POST --raw --http 10.17.24.163:5010/api/v1/cmd 
--jsonwrapper 'payload' --msg '
        {   "action": "run",
            "meta":  {
                "cmd":      "$execshell $selfpath/$selfexec --prefix test- --sleepLength 0 /share/incoming /share/outgoing",
                "auid":     "rudolphpienaar",
                "jid":      "simpledsapp-1",
                "threaded": true,
                "container":   {
                        "target": {
                            "image":            "fnndsc/pl-simpledsapp",
                            "cmdParse":         true
                        },
                        "manager": {
                            "image":            "fnndsc/swarm",
                            "app":              "swarm.py",
                            "env":  {
                                "shareDir":     "/home/tmp/share",
                                "serviceType":  "docker",
                                "serviceName":  "testService"
                            }
                        }
                }
            }
        }
'

coordination

timing can be complex...

PUSH data

separate coordinator service

WAIT!

EXEC on data

WAIT!

PULL data

WAIT!

coordination

coordinate

            "meta-store": {
                        "comment":      "The <meta-store> defines which paragraph to process to determine the <key> field to pass to <pfioh>. In this case, the <jid> field of the <meta-compute> will be used as the <key> field.",
                        "meta":         "meta-compute",
                        "key":          "jid"
            },

            "meta-data": {
                "remote": {
                        "comment":      "The <key> to use is a lookup in the <meta-store>.",
                        "key":          "%meta-store"
                },
                "localSource": {
                        "comment":      "The path containing data to process.",
                        "path":         "/neuro/users/rudolphpienaar/Pictures"
                },
                "localTarget": {
                        "comment":      "Once processed at the remote compute, return results to this path.",
                        "path":         "/neuro/users/rudolphpienaar/tmp/Pictures",
                        "createDir":    true
                },
                "specialHandling": {
                        "comment":      "This triggers some special processing in <pfioh> -- basically the <incoming> and <outgoing> directories are created and populated in a manner that the plugins expect.",
                        "op":           "plugin"
                },
                "transport": {
                    "mechanism":    "compress",
                    "compress": {
                        "encoding": "none",
                        "archive":  "zip",
                        "unpack":   true,
                        "cleanup":  true
                    }
                },
                "comment":              "The <service> name is hardcoded in the pfcon source and denotes the IP and port of the <pfioh> service.",
                "service":              "pangea"
            },

coordinate

            "meta-compute":  {
                "comment":  "The $ strings in the <cmd> are substituted with values found my running the plugin w/o any args. NB: the incoming and outgoing dirs need to be properly handled! In this example they are mapped from the <key> location in <pfioh> appropriately.",
                "cmd":      "$execshell $selfpath/$selfexec --prefix test- --sleepLength 0 /share/incoming /share/outgoing",
                "auid":     "rudolphpienaar",
                "jid":      "simpledsapp-1",
                "threaded": true,
                "container":   {
                        "target": {
                            "comment":          "The plugin to run. The <cmdParse>, if true, means substitute $ in the <cmd> string.",
                            "image":            "fnndsc/pl-simpledsapp",
                            "cmdParse":         true
                        },
                        "manager": {
                            "comment":          "The manager container to run, with relevant <env> settings.",
                            "image":            "fnndsc/swarm",
                            "app":              "swarm.py",
                            "env":  {
                                "meta-store":   "key",
                                "serviceType":  "docker",
                                "shareDir":     "%shareDir",
                                "serviceName":  "testService"
                            }
                        }
                },
                "comment":              "The <service> name is hardcoded in the pfcon source and denotes the IP and port of the <pfioh> service.",
                "service":              "pangea"
            }
        }

security

Medical data is constrained by many external factors
Logging and control
Single shutoff point
Communication pathways

HIPAA
Local regulatory
IRB

secure architecturally

secure communication

big data

Imaging
Genomics
Pathology

Input DICOM space
Processed result space
Structured clinical reporting

big data...

UI concepts

conclusion

Healthcare compute is at an inflection point
Lags larger computing -verse
Many opportunities and challenges exist

references... ChRIS

https://github.com/FNNDSC/ChRIS_ultron_backEnd

https://github.com/FNNDSC/ChRIS_ultron_frontEnd

references... services

```
https://github.com/FNNDSC/viewerjs
```
```
https://github.com/FNNDSC/gcjs
```
```
https://github.com/FNNDSC/fmjs
```
```
https://github.com/FNNDSC/toolbarjs
```
```
https://github.com/FNNDSC/rboxjs
```
```
https://github.com/FNNDSC/rendererjs
```
```
https://github.com/FNNDSC/thbarjs
```
```
https://github.com/FNNDSC/pman
```
```
https://github.com/FNNDSC/pfioh
```
```
https://github.com/FNNDSC/pfcon
```

references... viewers

```
https://goxtk.com
```
```
https://github.com/FNNDSC/ami
```

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

fin!

Thank you!

rudolph.pienaar@childrens.harvard.edu

Web apps..?

Simple, single-purpose
- Show static information: text and/or images
- Provide single-focus dynamic data
Complex, integrative, but still generically single-purpose
- Facebook
- Twitter
- Mobile: instagram, snapchat, whatsapp, etc...

Web-apps....

... can be

Web apps..?

Web apps...

are

Accessible from anywhere!
- Desktops, Laptops
- (Smart) Phones
- Tablets
Are "simple"
- require little end user maintenance
- just go to a link
but...
- Are typically not as "powerful" as traditional client apps.

Medical Image Viewers

How to view images...

... easily?

MedXT
Zebra-med
Cornerstone (Chris Chafey)
SliceDrop
MedView
mi2b2 Viewer

Medical Image Viewers

Viewer infrastructure...

ChRIS "reloaded..."

Web applications are increasingly more powerful, easy to use, and accessible

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

ChRIS "Ultron"... REST

overview

FNNDSC...

... software efforts

Compute infrastructure
- HPC
  - "front end" cluster
  - "back end" cluster
Data "movement"
- file system abstractions
- cloud-based access
Compute "movement"
- dockers

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
```

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

thank you...

ChRIS -- A Service for Collecting, Organizing, Processing, and Sharing Medical Image Data in the Cloud

By Rudolph Pienaar

ChRIS -- A Service for Collecting, Organizing, Processing, and Sharing Medical Image Data in the Cloud

A general overview of ChRIS

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ChRIS - A Service for Collecting, Organizing, Processing, and Sharing Medical Image Data in the Cloud

ChRIS

ChRIS -- A Service for Collecting, Organizing, Processing, and Sharing Medical Image Data in the Cloud

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