Handheld OCT Scanner

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    28-Apr-2015

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

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<p>ATLAS OCT</p> <p>Handheld OCT ScannerDr. Stephen Allen Boppart</p> <p>Tunaidi Ansari, Brian Baker, Casey Lewis, and Nickalus Zielinski</p> <p>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</p> <p>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.</p> <p>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</p> <p>2</p> <p>Acknowledgements ...................................................................... 26 Appendix 1: Atlas OCT MOU .................................................... 27 Appendix 2: Atlas OCT Project Plan ....................................... 33 Appendix 3: Atlas OCT Budget ................................................. 34</p> <p>3</p> <p>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.</p> <p>4</p> <p>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,</p> <p>5</p> <p>reports, reviews, and presentations. The Atlas OCT team decided upon two project objectives for the client, 1) A prototype device that collects OCT data associated with its physical position and 2) software to operate the device and construct images from the data and its source code, as well as objectives associated with the senior design class, including weekly progress reports and meetings, design reviews, presentations, and reports. The three aforementioned object (problem statement, mission statement, and project objectives) were used to form the body of a memorandum of understand (MOU) between the client and the team. The MOU was designed to serve as an informal contract between the two parties, which could be modified to suit the projects goals and the clients expectations, identifying and clarifying key areas of interest, including resources, and intellectual property, as well as serving as a mechanism to resolve disputes between the client and the team, should they arise. The MOU drafted and signed by team Atlas OCT and Dr. Stephen Boppart can be viewed in Appendix 1. In order to be able to stay on task, and accomplish all the goals that were determined on time, a project plan was put into place. The first step taken in order to prepare the project plan was to determine what steps needed to be taken and what order each of these needed to be done in. Additionally, the interdependencies were determined. The main areas that needed to be focused upon were researching different technologies and alternatives, gathering the materials, getting each individual task to work, and then to integrate all the different functions of our probe. After this was accomplished we set out to do some testing on the prototype, starting with phantoms, and then moving to live subjects. As the project moved forward, and setbacks were encountered, the project plan was continually updated and referred to in order to keep the project on task. The Project Plan can be found in Appendix 2. A budget was also developed for the Atlas OCT project. As initially stated, the Bioengineering department was willing to fund up to $500 for a single project, with a soft-cap at the $400 level. Our final budget included the following: $200 for a system to measure and track motion, $13 for a communication device, $100 for 2 hours of machine shop work, $30 for the SM1V05 OCT attachment (spacer), $10 for a case, $40 for a backup motion detection device, and $40 for various shipping costs. The estimated costs totaled $436.50, and the actual costs totaled $401.01. A copy of the final Atlas OCT budget is available in Appendix 3.</p> <p>6</p> <p>Design ProcessFunction DecompositionOur project was broken down into the following verb-noun objectives: Measure Parameter Some type of data must be acquired to calculate position and orientation Calculate Position The measured data must be converted to position and orientation Display Image The final result must be viewable Store Data The data must reside somewhere, whether it is kept on the probe and downloaded at once or streamed to the computer and stored there Combine Image and Position Data OCT and Position data must be used together to produce the finale output image Sweep Light over Area Different methods were available for broader data collection Communicate Data The measured data must somehow get from the probe to the computer Power Sensor The measurement unit must receive energy to perform its function Initiate Scan There must be a way of telling the system to begin taking data</p> <p>Concept EvaluationsWhile some of the decomposed function verb-noun pairs interacted, each category of concepts could, for the most part, be evaluated separately. Numerical analysis can be found in the Concept Evaluations excel sheet on the CD. Measure Parameter Measure Parameter was easily the most complex and influential concept to evaluate. Several options for obtaining data that could be used to calculate position were considered: a combination of accelerometers and gyroscopes, a camera on the probe looking at external visual markers either on the ceiling, or infra-red LEDs, an optical mouse, an articulated arm with angle sensors, a gyroscopic mouse, and laser positioning systems. These concepts were evaluated in terms of their availability, cost, size, and especially ease of implementation, ease of use, and estimated resolution. We looked for a solution that could track position accurately but fit in a compact form factor. Figures were found showing low resolutions for camera solutions, and optical mice and gyro mice just didnt have enough sensors to track position and orientation in 3D space. The laser positions system and articulated arm both seemed bulky and counter to the design input requirement of a handheld probe, and the articulated arm also was found to be too expensive to pursue, although its resolution was very high. In the end, a combination of accelerometer and gyroscopes was chosen.</p> <p>7</p> <p>Calculate Position Different languages were considered for doing the math required to turn the measured parameter data in position data. Specifically, MATLAB, Python, and microcontroller co...</p>

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