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pyMetris : a flexible endoscope tracker

                   Vincent Agnus

   Research Institute against Digestive Cancer (...
Medical Context
                                pyMetris
                          Python Benefit


Outline



      Medica...
Medical Context   IRCAD
                               pyMetris   New Surgical Procedures
                         Python ...
Medical Context   IRCAD
                               pyMetris   New Surgical Procedures
                         Python ...
Medical Context   IRCAD
                               pyMetris   New Surgical Procedures
                         Python ...
Medical Context   IRCAD
                                  pyMetris   New Surgical Procedures
                            P...
Medical Context   IRCAD
                                  pyMetris   New Surgical Procedures
                            P...
Medical Context   Overview
                                pyMetris   Tracking
                          Python Benefit    ...
Medical Context   Overview
                               pyMetris   Tracking
                         Python Benefit    Ap...
Medical Context   Overview
                              pyMetris   Tracking
                        Python Benefit    Appl...
Medical Context   Overview
                               pyMetris   Tracking
                         Python Benefit    Ap...
Medical Context   Overview
                              pyMetris   Tracking
                        Python Benefit    Appl...
Medical Context   Overview
                                pyMetris   Tracking
                          Python Benefit    ...
Medical Context   Overview
                               pyMetris   Tracking
                         Python Benefit    Ap...
Medical Context   Overview
                               pyMetris   Tracking
                         Python Benefit    Ap...
Medical Context   Overview
                               pyMetris   Tracking
                         Python Benefit    Ap...
Medical Context   Overview
                               pyMetris   Tracking
                         Python Benefit    Ap...
Medical Context   Overview
                               pyMetris   Tracking
                         Python Benefit    Ap...
Medical Context   Overview
                               pyMetris   Tracking
                         Python Benefit    Ap...
Medical Context   Overview
                               pyMetris   Tracking
                         Python Benefit    Ap...
Medical Context   Overview
                               pyMetris   Tracking
                         Python Benefit    Ap...
Medical Context   Context
                                 pyMetris   Productivity
                           Python Benefi...
Medical Context   Context
                               pyMetris   Productivity
                         Python Benefit   ...
Medical Context   Context
                            pyMetris   Productivity
                      Python Benefit    Used ...
Medical Context
                              pyMetris
                        Python Benefit


Conclusion + Perspectives

...
Medical Context
          pyMetris
    Python Benefit




Thank you for your attention




   Vincent Agnus     pyMetris : ...
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PyMetris : A flexible Endoscope Tracker

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A python application for tracking a flexible endoscope using a magnetic tracking system

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Transcript of "PyMetris : A flexible Endoscope Tracker"

  1. 1. pyMetris : a flexible endoscope tracker Vincent Agnus Research Institute against Digestive Cancer (IRCAD) Strasbourg EuroScipy, 11 july 2010, Paris, France
  2. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 26. Medical Context pyMetris Python Benefit Thank you for your attention Vincent Agnus pyMetris : a flexible endoscope tracker
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