Handheld OCT Scanner

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Senior design paper detailing research and development of an innovative handheld OCT scanner.

Transcript of Handheld OCT Scanner

ATLAS OCT

Handheld OCT ScannerDr. Stephen Allen Boppart

Tunaidi Ansari, Brian Baker, Casey Lewis, and Nickalus Zielinski

Table of Contents Introduction .................................................................................... 4 The Project ..................................................................................... 5 Design Process ................................................................................ 7Function Decomposition ................................................................................................. 7 Concept Evaluations ....................................................................................................... 7 Measure Parameter...................................................................................................... 7 Calculate Position ....................................................................................................... 8 Display Image ............................................................................................................. 8 Store Data.................................................................................................................... 8 Combine Image and Position Data ............................................................................. 8 Sweep Light over Area ............................................................................................... 8 Communicate Data...................................................................................................... 8 Power Sensor .............................................................................................................. 9 Initiate Scan ................................................................................................................ 9 Configuration Designs .................................................................................................... 9

As-Built Documentation .............................................................. 11Probe ............................................................................................................................. 11 Position Tracking Hardware ......................................................................................... 13 Bluetooth Dongle ...................................................................................................... 13 Original IMU ............................................................................................................ 13 Wiimote..................................................................................................................... 15 New Atomic IMU ..................................................................................................... 16 Input Software ............................................................................................................... 16 IMUReader ............................................................................................................... 17 WiimoteReader ......................................................................................................... 19 MATLAB atlasoct_main.m ................................................................................... 20 MATLAB reader.m................................................................................................ 20 Integration Software...................................................................................................... 20 MATLAB calibrator.m .......................................................................................... 20 MATLAB calibrator2.m ........................................................................................ 20 MATLAB integration.m going from measurements to positions ....................... 21 MATLAB turner.m rotating the position data .................................................... 21 MATLAB revive.m generate a 3-d representation of the sample ....................... 21 MATLAB slicer.m create a series of usable images........................................... 22 ImageJ MedNuc-OrtView plugin Putting it all together..................................... 22 Design Verification ........................................................Error! Bookmark not defined. Design Validation ..........................................................Error! Bookmark not defined.

Plan/Project Critique ................................................................... 23Probe ............................................................................................................................. 23 Position Tracking Hardware and Input Software.......................................................... 23 Integration Code / Software .......................................................................................... 24 Putting It All Together Combining the OCT and position data ................................. 24

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Acknowledgements ...................................................................... 26 Appendix 1: Atlas OCT MOU .................................................... 27 Appendix 2: Atlas OCT Project Plan ....................................... 33 Appendix 3: Atlas OCT Budget ................................................. 34

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IntroductionThe following report is a detailed documentation of the Bioengineering senior design project by Atlas OCT. This team is comprised of Tunaidi Ansari, Brian Baker, Casey Lewis, and Nickalus Zielinski. The report covers the work of the Atlas OCT team over the Fall 2008 and Spring 2009 semesters under the direction of the instructor, Dr. Michael Haney, and the client, Dr. Stephen Boppart of the Biophotonics Imaging Laboratory at the Beckman Institute for Advanced Science and Technology. The goal of the teams design project was to create a functional prototype for a hand-held OCT scanner, capable of tracking position as well as collecting OCT data, and assimilating the two data sets to produce two dimensional cross sectional scans or three dimensional volume scans. This report contains an explanation of the project and its goals, documentation of the design phase, a description of the completed prototype as-built, and a discussion and evaluation of the product and process by which it was created.

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The ProjectOn October 7th, 2008, Dr. Stephen Boppart presented to the team two possible projects involving optical coherence tomography (OCT) technology. The project the team chose to develop was titled Gyroscopic Three-Dimensional Scanner for Optical Coherence Tomography and involved several scientific disciplines, including OCT, optics, software engineering, and electronics, as well as special packaging concerns, to insure that the device could be operated in hand-held manner. The designs goal was a portable and modular OCT imaging system, which would allow for a compact and portable system which could be used in a clinical setting, as well as a user-friendly software interface, and a probe that could attach to modular beam delivery devices. The hand-held nature of the probe would allow for scanning in transverse or a three dimensional manner, creating either cross-sectional images or 3-D volume scans. One initial solution provided by the client at the conception of the design team was a previously purchased USB mouse which contained gyroscopes, as well as the traditional optoelectronic sensor in the form of a LED (light emitting diode) which tracks movement over a surface in two dimensions using an optical flow estimation algorithm. Although this route received a strong recommendation from the client from the very onset of the project, the team did not choose this method, and the reasons for which this decision was made will be discussed at length later in the report. From the descriptions provided and several additional meetings with the client and his research team, the design team developed a problem statement, mission statement, and a list of project objectives. Additionally, the team developed a project plan, spanning the two semesters allocated toward this project, as well as a budget. The problem statement is an attempt to identify the problem at hand, as well as the desired end state of the project, what obstacles are preventing this from being reached, and how a successful solution to the problem will be identified. The problem statement developed by Atlas OCT is as follows: To obtain Optical Coherence Tomography (OCT) scans from a handheld device, position tracking data must be integrated with OCT data to reconstruct a two dimensional image. Such a device must consistently and accurately track its position so that a computer may assemble images from the data. Currently, there is no such device that incorporates position tracking to create images from a manual scanner. The mission statement is designed to identify what the team will be doing, as well as for whom (the client) and how this will be accomplished. The mission statement developed by Atlas OCT is as follows: Atlas OCT will provide Dr. Stephen Boppart and the Biophotonics Imaging Laboratory at the Beckman Institute for Advanced Science and Technology with a physical handheld OCT scanner that tracks its position, with supporting software to assemble two dimensional images from the collected data. If time permits, generation of three dimensional images and publishing of research shall be attempted. This will be achieved through regular meetings with Dr. Stephen Boppart and the senior design team, and interaction with other members of the Biophotonics Imaging Laboratory. Finally, a listing of the project objectives was developed, including the projects goals and outcomes, as well as any deliverables, including plans, drawing, devices,

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reports, reviews, and presentations. The Atlas OCT team decided upon two project objectives for the client, 1) A pr