pymetris : a flexible endoscope tracker
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pyMetris : a flexible endoscope tracker
Vincent Agnus
Research Institute against Digestive Cancer (IRCAD)Strasbourg
EuroScipy, 11 july 2010, Paris, France
Medical ContextpyMetris
Python Benefit
Outline
Medical Context :
IRCADNew surgical procedures
pyMetris
FunctionalitiesApplications in surgery
Benefits using Python
Productivity
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
IRCADNew Surgical ProceduresNatural Orifice Transluminal Surgery (NOTES)
Research Institute against Digestive Cancer
Research Institute against Digestive Cancer
Private institute founded in 1994 by Pr. Marescaux
A Training Center
4000 surgeons/year
A Research Center
Cancer biology
Robotic surgery
Computer aided surgery
New surgical techniques
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
IRCADNew Surgical ProceduresNatural Orifice Transluminal Surgery (NOTES)
Research Institute against Digestive Cancer
Research Institute against Digestive Cancer
Private institute founded in 1994 by Pr. Marescaux
A Training Center
4000 surgeons/year
A Research Center
Cancer biology
Robotic surgery
Computer aided surgery
New surgical techniques
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
IRCADNew Surgical ProceduresNatural Orifice Transluminal Surgery (NOTES)
Medical Context
Standard Surgical Procedures (1990)
Minimally Invasive Surgery :
small incisions
(long) tools
camera
Patient Benefits
painless
small scars
Surgeon Challenge
referencial : decoupling eye(camera) – hands(tools)
camera : loss of depth perception + parasite motion
tools : manipulationVincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
IRCADNew Surgical ProceduresNatural Orifice Transluminal Surgery (NOTES)
Natural Orifice Transluminal Surgery (NOTES)
New Surgical Procedure : NOTES (2005)
use of a flexible endoscope
insert through natural orifice: mouth,urethra, anus
internal incision: stomach, vagina,colon
Patient Benefits
no external scars
fast scaring – less infection
Surgeon Challenge
manipulation of endoscope
localization of endoscope
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
IRCADNew Surgical ProceduresNatural Orifice Transluminal Surgery (NOTES)
Natural Orifice Transluminal Surgery (NOTES)
New Surgical Procedure : NOTES (2005)
use of a flexible endoscope
insert through natural orifice: mouth,urethra, anus
internal incision: stomach, vagina,colon
Patient Benefits
no external scars
fast scaring – less infection
Surgeon Challenge
manipulation of endoscope
localization of endoscope
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Description
Main Functionalities
GPS for endoscope :
display in real-time endoscope shape
display a patient model
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Description
Extra Functionalities
record/replay endoscope position → analyze
place a target/path (saved endoscope position)
display a virtual horizon – roll information
extensible using scripts
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Description
Endoscope Tracking
NDI Aurora R© Electromagnetic Measurement System
8 probes 5cm spaced along a cable → 3D position anddirection via RS232
Diameter cable 2.2mm ⇒ insertable in operating channel ofendoscope
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Applications
Medical Use
Tests are currently performed only on live pig
Certificatation of conformity for human use in progress
Applications/Validations
Colonoscopy
Navigation
Gastric Exit Point in Gastrotomy
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Applications : Colonoscopy
Objectives
view endoscope loop ⇒ avoid colon injuries
can compute polyp distance
Results
no magnetic field disturbance in operative room
software robustness
but pig colon6= human colon (more mobile,fragile)Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Applications : Navigation
Objectives
quantify the benefits using pyMetris :
time to reach targetsurgeon feebackendoscope path variation
Results
abdominal cavity : no significant benefit (visual reference)
find duodenal papilla ( without/with pyMetris 5min/1min )
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Applications : Navigation
Objectives
quantify the benefits using pyMetris :
time to reach targetsurgeon feebackendoscope path variation
Results
abdominal cavity : no significant benefit (visual reference)
find duodenal papilla ( without/with pyMetris 5min/1min )
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Applications : Navigation
Objectives
quantify the benefits using pyMetris :
time to reach targetsurgeon feebackendoscope path variation
Results
abdominal cavity : no significant benefit (visual reference)
find duodenal papilla ( without/with pyMetris 5min/1min )Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladderas horizontal as possiblefrontal access
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladderas horizontal as possiblefrontal access
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladderas horizontal as possiblefrontal access
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladderas horizontal as possiblefrontal access
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladderas horizontal as possiblefrontal access
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
OverviewTrackingApplications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladderas horizontal as possiblefrontal access
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
ContextProductivityUsed Packages
Python Benefit : Context
Development Context
rapid prototyping
functionality requirements updated at each meeting
low availability of surgeons
Resources
FrameWork for Software Production Line (fw4spl)
C++ libraries, multi-OScomponent-oriented architecture + role-based programminghttp://code.google.com/p/fw4spl/ (LGPL)
construction tools : sconspiracy
http://code.google.com/p/sconspiracy/ (BSD)
freeware VRRender http://www.ircad.fr/softwares/
1 Senior C++ developer ⇒ Python used
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
ContextProductivityUsed Packages
Python Benefit : Productivity
Python Benefit
easy to learn
concise langage : pyMetris < 1000 lines of code
reflexive langage : code completion in editor
interpreted language :
improve productivity (no cycle : compiling-testing)live-recoding during meeting, in OP roomscript : new functionalities (use execfile())
Packages :
all batteries includedexternal packages working out of the boxbinding of c++ library (wx,VTK)
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
ContextProductivityUsed Packages
Python Benefit : Used Packages
pyMetris
Rendering
Analysis
cPickle
Tracking
Softwares
NumPy + SciPyIPython
Eric IDESerialization
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
Conclusion + Perspectives
Conclusion
medical application
rapid prototyping thanks to Python
complete toolchain
Perspectives
thread the application
use mayavi, tvtk ?
integration of video → Augmented Reality
Python integration in fw4spl
Vincent Agnus pyMetris : a flexible endoscope tracker
Medical ContextpyMetris
Python Benefit
Thank you for your attention
Vincent Agnus pyMetris : a flexible endoscope tracker
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