PyMetris : A flexible Endoscope Tracker

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


Python Benefit

IRCADNew Surgical ProceduresNatural Orifice Transluminal Surgery (NOTES)

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



Python Benefit




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



Python Benefit


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


Python Benefit


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



Python Benefit


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



Python Benefit

OverviewTrackingApplications

pyMetris Description

Main Functionalities

GPS for endoscope :

display in real-time endoscope shape

display a patient model



Python Benefit



Extra Functionalities

record/replay endoscope position → analyze

place a target/path (saved endoscope position)

display a virtual horizon – roll information

extensible using scripts



Python Benefit



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



Python Benefit


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



Python Benefit


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


Python Benefit


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 )



Python Benefit



Objectives



Results


find duodenal papilla ( without/with pyMetris 5min/1min )



Python Benefit



Objectives



Results


find duodenal papilla ( without/with pyMetris 5min/1min )Vincent Agnus pyMetris : a flexible endoscope tracker


Python Benefit


pyMetris Applications : Gastric Exit Point

Objectives

find the best gastrotomy for a cholecystectomy :

close enough to gallbladderas horizontal as possiblefrontal access



Python Benefit



Objectives





Python Benefit



Objectives





Python Benefit



Objectives





Python Benefit



Objectives





Python Benefit



Objectives





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


http://code.google.com/p/fw4spl/

http://code.google.com/p/sconspiracy/

http://www.ircad.fr/softwares/


Python Benefit


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)



Python Benefit


Python Benefit : Used Packages

pyMetris

Rendering

Analysis

cPickle

Tracking

Softwares

NumPy + SciPyIPython

Eric IDESerialization



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



Python Benefit

Thank you for your attention


Date post:	05-Aug-2015
Category:	Health & Medicine
Upload:	vincent-agnus
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PyMetris : A flexible Endoscope Tracker

Health & Medicine