The document describes pyMetris, a flexible endoscope tracking system developed at the Research Institute against Digestive Cancer (IRCAD). PyMetris uses electromagnetic tracking to determine the position and orientation of probes placed along an endoscope as it is inserted through the body. It provides surgeons with visualization of the endoscope's shape and position to assist with new minimally invasive surgical techniques. Python was used to develop pyMetris due to its rapid prototyping capabilities, which allowed functionality to be updated quickly based on surgeon feedback. The system has been tested in various surgical applications including colonoscopy and locating anatomical structures.

1. pyMetris : a flexible endoscope tracker
Vincent Agnus
Research Institute against Digestive Cancer (IRCAD)
Strasbourg
EuroScipy, 11 july 2010, Paris, France

2. Medical Context
pyMetris
Python Benefit
Outline
Medical Context :
IRCAD
New surgical procedures
pyMetris
Functionalities
Applications in surgery
Benefits using Python
Productivity
Vincent Agnus pyMetris : a flexible endoscope tracker

3. Medical Context IRCAD
pyMetris New Surgical Procedures
Python Benefit Natural 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

4. Medical Context IRCAD
pyMetris New Surgical Procedures
Python Benefit Natural 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

5. Medical Context IRCAD
pyMetris New Surgical Procedures
Python Benefit Natural 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 : manipulation
Vincent Agnus pyMetris : a flexible endoscope tracker

6. Medical Context IRCAD
pyMetris New Surgical Procedures
Python Benefit Natural 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

7. Medical Context IRCAD
pyMetris New Surgical Procedures
Python Benefit Natural 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

8. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
pyMetris Description
Main Functionalities
GPS for endoscope :
display in real-time endoscope shape
display a patient model
Vincent Agnus pyMetris : a flexible endoscope tracker

9. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
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

10. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
pyMetris Description
Endoscope Tracking
NDI Aurora R Electromagnetic Measurement System
8 probes 5cm spaced along a cable → 3D position and
direction via RS232
Diameter cable 2.2mm ⇒ insertable in operating channel of
endoscope
Vincent Agnus pyMetris : a flexible endoscope tracker

11. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
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

12. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
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 colon= human colon (more mobile,fragile)
Vincent Agnus pyMetris : a flexible endoscope tracker

13. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
pyMetris Applications : Navigation
Objectives
quantify the benefits using pyMetris :
time to reach target
surgeon feeback
endoscope path variation
Results
Vincent Agnus pyMetris : a flexible endoscope tracker

14. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
pyMetris Applications : Navigation
Objectives
quantify the benefits using pyMetris :
time to reach target
surgeon feeback
endoscope path variation
Results
abdominal cavity : no significant benefit (visual reference)
Vincent Agnus pyMetris : a flexible endoscope tracker

15. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
pyMetris Applications : Navigation
Objectives
quantify the benefits using pyMetris :
time to reach target
surgeon feeback
endoscope 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

16. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladder
as horizontal as possible
frontal access
Vincent Agnus pyMetris : a flexible endoscope tracker

17. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladder
as horizontal as possible
frontal access
Vincent Agnus pyMetris : a flexible endoscope tracker

18. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladder
as horizontal as possible
frontal access
Vincent Agnus pyMetris : a flexible endoscope tracker

19. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladder
as horizontal as possible
frontal access
Vincent Agnus pyMetris : a flexible endoscope tracker

20. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladder
as horizontal as possible
frontal access
Vincent Agnus pyMetris : a flexible endoscope tracker

21. Medical Context Overview
pyMetris Tracking
Python Benefit Applications
pyMetris Applications : Gastric Exit Point
Objectives
find the best gastrotomy for a cholecystectomy :
close enough to gallbladder
as horizontal as possible
frontal access
Vincent Agnus pyMetris : a flexible endoscope tracker

22. Medical Context Context
pyMetris Productivity
Python Benefit Used 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-OS
component-oriented architecture + role-based programming
http://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

23. Medical Context Context
pyMetris Productivity
Python Benefit Used 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 room
script : new functionalities (use execfile())
Packages :
all batteries included
external packages working out of the box
binding of c++ library (wx,VTK)
Vincent Agnus pyMetris : a flexible endoscope tracker

24. Medical Context Context
pyMetris Productivity
Python Benefit Used Packages
Python Benefit : Used Packages
Tracking Rendering
pyMetris
Softwares Analysis
IPython NumPy + SciPy
Eric IDE
Serialization
cPickle
Vincent Agnus pyMetris : a flexible endoscope tracker

25. Medical Context
pyMetris
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

26. Medical Context
pyMetris
Python Benefit
Thank you for your attention
Vincent Agnus pyMetris : a flexible endoscope tracker