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- Rudolph Pienaar (Boston Children's Hospital)
- Jorge Bernal (Boston Children's Hospital)
- Nicolas Rannou (Eunate Technology)
- Anneke Meyer (University of Magdeburg, Germany)
- Introduce the CHRIS platform.
- Containerize a slicer app
- Run app in CHRIS framework on the Massachusetts Open Cloud
- Identify a candidate slicer app to use.
- Containerize app in CHRIS-compliant structure.
- Deploy to CHRIS distributed instance running locally.
- Deploy to CHRIS distributed instance running on the Massachusetts Open Cloud.
- Identified a trained prostate segmenter from Anneke Meyer.
- Created a CHRIS plugin repository and docker hub build for this app:
- Successfully ran the segmenter plugin using CHRIS services distributed across localhost and a manager listening on lab website.
pfurl --verb POST --raw --http ${HOST_IP}:5005/api/v1/cmd \
--httpResponseBodyParse --jsonwrapper 'payload' \
--msg \
'{
"action": "coordinate",
"threadAction": true,
"meta-store": {
"meta": "meta-compute",
"key": "jid"
},
"meta-data": {
"remote": {
"key": "%meta-store"
},
"localSource": {
"path": "/home/rudolphpienaar/src/pl-neuproseg/data/ProstateX-0029"
},
"localTarget": {
"path": "/home/rudolphpienaar/tmp/output",
"createDir": true
},
"specialHandling": {
"op": "plugin",
"cleanup": true
},
"transport": {
"mechanism": "compress",
"compress": {
"encoding": "none",
"archive": "zip",
"unpack": true,
"cleanup": true
}
},
"service": "fnndsc"
},
"meta-compute": {
"cmd": "$execshell $selfpath/$selfexec --multistream /share/incoming /share/outgoing",
"auid": "rudolphpienaar",
"jid": "89",
"threaded": true,
"container": {
"target": {
"image": "fnndsc/pl-neuproseg",
"cmdParse": true
},
"manager": {
"image": "fnndsc/swarm",
"app": "swarm.py",
"env": {
"meta-store": "key",
"serviceType": "docker",
"shareDir": "%shareDir",
"serviceName": "89"
}
}
},
"service": "fnndsc"
}
}
- Source code: https://github.com/FNNDSC/pl-neuproseg
- Documentation: https://github.com/FNNDSC/pl-neuproseg/wiki
- Test data: https://github.com/FNNDSC/pl-neuproseg