## ABRD5188 --- Biomedical Optics in Taiwan --- Summer-II 2014

Biomedical Optics: Prof. Charles A. DiMarzio | TA Joseph Hollmann | Syllabus
Chinese Cultures in Taiwan: Prof. David Blundell | TA Stephanie Noelle Micham | Syllabus
Tentative Course Calendar (.pdf)
Lodging: Taida Zunxian Huiguan

This is the website for Biomedical Optics in Taiwan, a program of the Dialogues of Civilization Program at Northeastern University. Our goals for this summer are (1) to study biomedical optics along with students and faculty at the National Taiwan University for 4SH of credit as a Technical Elective, (2) to study Taiwanese Culture for 4SH of credit as a social science or humanities elective, and (3) to have the experience of living for five weeks in Taipei and interacting with engineers and others in that city.

Announcements (Updated 12 August 2014)

(12 August 2014) Here's an interesting article about night markets in the San Gabriel Valley of California. http://www.pasadenastarnews.com/events/20140811/626-night-market-to-take-place-this-weekend-hours-have-been-extended.

(9 August 2014) Here's a map of today's trip. I'll post some pictures with it later.

(7 August 2014) The paper Joseph mentioned in class is posted at this link.

The homework for this week includes two computational tasks.

• Pick some optical properties of dermis at some wavelength, and run MCML on an single semi-infinite layer. to determine the absorbed power per unit volume as a function of z and r, as well as the diffusely reflected power per unit area as a function of r. Ensure the medium above the tissue has the same index of refraction as the tissue.
• Then write Matlab code to compute the same two outputs in the diffusion approximation.
• This part is important: Discuss the similarities and differences between your two calculations.

(5 August 2014) Three items of importance. First, here is our schedule updated yesterday by April. Second, here are some ideas for major projects. Basically they seem to divide into two categories.

Processing existing data: (1) contour tracking lung images, (2) spectral unmixing of hemoglobin in bone, (3) comparing 3-photon fluorescence to confocal reflectance in melanin.

Computational modeling: (1) Absorption in particles using extensions of Mie scattering. (2) Light propagation in bone using Monte-Carlo or diffusion equations (3) Detection of optical changes in tissue under ultrasound heating (4) Computational modeling of almost any imaging modality in the chart below.

(4 August 2014) Here is the file to compute optical properties of skin. For the homework, use the dermis properties for a single (infinitely thick) layer. skin_opt.m

(3 August 2014) Our new location for all classes is the cafe at 84.6 Xinsheng Road Section 3. Don't try to put this address into Google maps as it goes to the wrong place. Here is a map of walking directions. http://goo.gl/maps/fYwcR. There are two parallel stairways. Take the one closest to the Adidas store and go to the third floor. There is a glass sign that says "Idea Cafe" which is likely to be open.

(31 July 2014) Tomorrow our class is in 203 Ming Da (same building as today but a different room). I will end promptly at noon. Please yell at me if I do not. We have hired a bus for the Ying Ge pottery trip, and it departs the hotel at 1:00 promptly. Please be on time.

(31 July 2014) Here is the promised Matlab function, bhmie.m If you want to use the online calculator, it is at http://omlc.org/calc/mie_calc.html. As I mentioned in class, there is a wealth of information on this site. Look at the links on the left of the page and you may want to bookmark the home page. Another useful link, http://refractiveindex.info has some good data on index of refraction. If you want a material that is really absorbing, here's a function that generates the complex index of refraction of melanin; melanin.m . As always, use the help function (help melanin) for instructions, and of course feel free to ask if you have questions. I didn't write this code for public consumption, and I will admit that it isn't particularly "user friendly."

(30 July 2014) Jimmy found an announcement of this event, and asked Christie for the location. She provided the website, thinking that more of you might be interested. National Taiwan Science Education Center. It looks like an easy walk from Shilin Station on the Red Line. Check their transportation page for bus lines. This might be a good outing for this weekend.

(29 July 2014) The matlab and data files I used in class for the spectroscopy talk are in bonespec.zip . Type help bonespec1 for instructions. Let me know if anything isn't clear. There are 3 data files; The differences are in the location of the detector. P1 is 10 mm from the source, P2 is 15, and P3 is 20. The greater spacings should, as we discussed in class, sample at greater depth.

(Mon, 28 July 2014) Here is the schedule for our trip to Yingge this coming Friday. Thanks to April for making this happen.

(27 July 103) Remmber that we meet in 114 EE Building 2 on Monday. I'll talk about spectroscopy. Let's plan to do the talks on biology for Chapters 1 and 5 on Tuesday (about 1 hour for each chapter), and 6 and 20 on Wednesday. I'll end the week talking about light scattering in random media like biological tissue. I think Thursday I'll introduce scattering from a single particle and then build up to the strong multiple scattering that we find in tissue. That's a slight revision of the original syllabus.

(22 July 103) Actually we learned today from Prof. Blundell that this is Year 103 in Taiwan, so I'm posting with the correct date. First, the Matlab file and a couple of required data files that I discussed in class today are posted in the matlab directory. Start Matlab in a directory with all these files and type "hbh2o" and it should work. I think I put up all the files needed. If it doesn't work, let me known.

Second, Typhoon Matmo is due to arrive tomorrow and NTU classes are cancelled. We'll plan to meet at the big table in the lobby at 9:30 for the Optics class. We'll decide what to do about the afternoon after we see what happens in the morning.

(20 July 2014) I'll post occasional comments and pictures Here.

(18 July 2014) Goodmorning! Get your boarding pass and check your bags, and come through security. We are gathering at Gate B22 for our flight to SFO.

(17 July 2014) Tomorrow is our departure day. I'll see you all at the airport, and we have a couple hours to hang out at SFO. If I recall correctly, SFO has free wireless. When we arrive at TPE, each of us will go through customs. After that, there is a currency exchange where you may want to pick up some New Taiwan Dollars. When we leave the controlled area, look for Stephanie, who will be holding a CIEE sign. She has a bus to take us to the hotel and assist us with checkin. Get a good night's sleep Saturday, and we'll meet in the hotel lobby at 9:30AM Sunday to walk to orientation. Wear your walking shoes then.

(15 July 2014) Joseph has arrived in Taiwan, and has a couple bits of advice. First, bring snacks for the SFO flight. Second, do not get any Taiwan currency before leaving (But I've already gotten some before I heard this). Quoting Joseph, "I checked in SF and it would have cost me \$40 extra dollars (versus here) to change \$200. There are a couple currency exchange booths just past customs that we can use."

I will be arriving at Logan by subway, and should be in the United Terminal at 6:20.

(10 July 2014) For those of you visiting a doctor in preparation for the trip, I'm not going to give advice on immunizations, but if you tell the doctor that you will be living in Taipei, possibly with an occasional trip outside the city to other parts of Taiwan, you should get good advice. For myself, I'm not getting anything special for this trip.

Disability Resources: One of our students is registered as a note-taker with the Disability Resource Center. If you need this service and are connected to the DRC, let me know, and we can make it happen.

(9 July 2014) Our travel information is posted here. Note that flight numbers and times have changed a little bit since we last discussed them. Plan to arrive at the airport by 6AM. You can obtain your own boarding pass and check baggage as needed.

(26 June 2014) There is a tentative syllabus for each of the two courses posted above.

(25 June 2014) Our contractor in Taipei will get us SIM cards for our phones. If you want one let me know before Monday. For more info, see phonecard.txt.

(18 Apr 2014) This is the beginning of the website for the course. As I get them ready, I'll post the syllabus along with other information and reminders. Plan to check here frequently for updates. For the moment, I have the tentative schedule posted. Keep in mind that it is still in planning. I'll add the missing details, and of course things might change. We're looking forward to a great summer.

Supporting Material

Getting Around. The subway: Taipei Metro Map . Our station is Gongguan (on the Green line, just like Northeastern)
The campus: National Taiwan University
Lodging: Taida Zunxian Huiguan

Matlab help: Note that there is a Matlab TA available to help with any Matlab problems. Check https://gazette.coe.neu.edu/?q=content/mathworks-ta-office-hours-spring-2014 for hours.

ABOUT THE BACKGROUND: My favorite winter passtime is skiing. I put this background together from a detail of a photograph taken at Park City, in 2003. There are four copies in different orientations so that the tracks (and more importantly, the brightness levels) line up as the pattern repeats.