Spring 2012: Jonathan Gootenberg Journal

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This is based off of Journal Guidelines.

Week 1 (2/6-2/12)

  1. What do you want to get out of 20.345?
    In a broad sense, I hope to get an understanding for principles of good design and engineering, which will ultimately make me a better engineer, both of experiments and of instrumentation. In a more specific sense, I hope to familiarize myself with new methods of design, such as CAD and microfluidics, and potentially develop a novel instrument.
  2. What are your areas of interest?
    I have fairly broad interests, ranging from optics to microfluidics to circuit design. I'm also very interested in the biological underpinnings, but I feel that this class is less focused on that.

Week 2 (2/13-2/19)

I began a tiny bit of work on movement of the stage for the center determining code.

Worked with Marie to prepare some bead samples. Because I previously took 20.309, I will probably pursue an alternative project.

Began working on my multiple-targeting timeshared optical trap with galvo mirrors. It will have a single beam expander after the galvo mirrors. I need to order the achromatic doublet lenses for the IR laser.

Week 3 (2/20-2/26)

Ordered lenses. Misplaced lenses. Reordered lenses. Took galvos from the confocal microscope, placed them in the beam path. Started aligning beam with green laser.

Week 4 (2/27-3/4)

Drew MIT seal on slide at 100x with green laser. Replaced optics with IR compatible achromats. Replaced green laser with IR laser, aligned beam.

Week 5 (3/5-3/11)

Not yet starting PSF lab

Week 6 (3/12-3/18)

Started to work on PSF lab. There was a bug in the code, and the stage would not move. Will revisit after Spring break, possibly rewrite the code.

Week 7 (3/19-3/25)

  1. What is the most important thing you accomplished during the first week of your project?
    I read the literature regarding 3D STORM and the necessary modifications that need to be made to the TI-Eclipse body to prepare it for 3D microscopy. I also read a little bit about techniques for reconstruction in software.
  2. What three things do you plan to accomplish in the next week?
    Because the TI-Eclipse body is not coming in for a while, I am going to try to model the optics/design in silico to help with the design later. I will try to obtain a CAD model of the microscope, and I may model the optics in software as well. Lastly, I want to read more about the software and begin drafting code.
  3. What three things do you plan to accomplish in the next month?
    Hopefully, the microscope body will be delivered within a month. Once the microscope is here, I can begin retrofitting it for STORM by switching in the cylindrical lens and adding the driving and fluorescence LEDs. Finally, I will develop the code for imaging.

Week 8 (3/26-4/1)

  1. Did you enjoy Spring Break?
    I did enjoy Spring Break. I went to Miami-lots of sun.

Week 9 (4/2-4/8)

  1. What is the riskiest element of your project? What is your backup plan if that element fails?
    The biggest risk in this project is its failure to fit to the timeline due to shipping related issues. It is possible that the TI-Eclipse will not ship by May, and I will not be able to even start my project. In this case, I will work will Vinnie on the holographic optical trap, which is a logical extension of my previous project. (This ended up happening).
  2. List two skills you will have to learn in order to complete your project.
    I will need to learn how to code in Java most likely to write the image analysis fast enough to do STORM. I will also have to learn to build a microscope with precision that exceeds the current commercial supe-rresolution microscopes.
  3. What companies make products related to your project? Whose products are the best?
    There are several commercially available super-resolution microscopes in STED, 4pi, and STORM variants. The best of these is most likely the STORM microscope manufactured by Nikon, the N-STORM. The N-STORM has 3-D capabilities and <100nm resolution. However, it costs nearly half a million dollars.

Week 10 (4/9-4/15)

  1. List at least five resources that have helped you. Your list may include papers, documentation,, textbooks, videos, downloaded code, or people who are not members of the teaching staff.
    Note: I have switched to the SLM optical trap.
    • I have used Albert Mao's senior thesis from Duke to modify the LitePro 580 Projector into a functional SLM. So far, we have not been able to get the LitePro to interact with the computer, but we may be able to fix that by modifying the cable.
    • Hologram code from University of Glasgow that allows for the 3-D control of multiple beads. We have yet to find if it works or not
    • “A Revolution in Optical Manipulation” – Grier et. al. This paper describes some of the basics of multiple optical trapping.
    • “Interactive Approach to Optical Tweezer Control” – Leach et. al. This paper describes some of the possible interfaces.
    • “The Generalized Phase Contrast Method and its Applications” – Gluckstad et. al. This paper discusses the history of GPC and lays the foundations for a majority of the current work in GPC and multiple trapping
  2. What was the most fun part of your project so far?
    The most fun part of the project so far was taking apart the projector piece by piece. It's interesting to see how the projector functions and the different failsafes that go into preventing overheating or other malfunctions.
  3. What task are you procrastinating the most?
    We have not started to fabricate or design waveguides, since we are more concerned about the development of the optical trap at first.

Week 11 (4/16-4/22)

  1. List at least three statistical techniques you plan to use.
    When we have the trap working, we will most likely use both linear and non-linear fits to determine the trap stiffness. We will also use Least-Squares approximations to develop the SLM patterns necessary for our desired patterns.
  2. Generate simulated data sets and test these techniques.
  3. What was the part of the project that you originally didn't think was important, but now has become a major task?
    It is becoming clear that the attachment of the projector to the computer will not be trivial. We have not yet gotten the projector to recognize the computer. Thankfully, we used the backup projector to determine this before any additional time was wasted.

Week 12 (4/23-4/29)

  1. Is there any part of your project that you now realize is not so important, and should have been skipped?
    I now realize that the rewiring of the 26-pin connector was not important at all, and that we have been wasting numerous hours taking the 26-pin cable apart. On the brighter side, this has shown me a fair amount about how wires work.
  2. What "unwritten knowledge" have you found out in the process of conducting your project (e.g., the kind of thing that never gets described in a book or paper, but you have to experience to understand)?
    I have found out unwritten knowledge bout how to probe the pins of a connector to map them to the different wires using a voltmeter. This may be written somewhere, but it seems like a common yet unwritten ability.
  3. Design a mathematical model, a simulation, or small pilot project, which takes no longer than 3 days, to reduce the risk of the remaining part of your project.
    We are using the green laser pilot project to reduce the risk of the IR final project

Week 13 (4/30-5/6)

  1. What is the biggest thing you would have done differently in your project, given what you've learned throughout your project so far?
    I woud have purchased the Video connector for the projector rather than the 26-pin connector. This change would have saved two days of troubleshooting, which could have been put into the development of the beam path.
  2. Instruments often require a biological demonstration to make their value clear. What would the most compelling demonstration of the power of your technology be? What will you do during the class period?
    I think that a possible use for the coupled optical waveguides/arbitrary optical trapping would be to stimulate optogenetic triggerable cytoskeleton cells, such as photoswitchable Cdc42 in planes parallel to the dish. This behavior would be novel.
  3. Reflect upon your pilot project from the previous week: did you carry it out? Why or why not?
    We are still implementing the green laser beam. It has been fairly successful.

Week 14 (5/7-5/13)

  1. If you had twice the time to do the project, what would you differently? What about if you had half the time? How does this thinking change your actual plans?
    In both cases, I would have worked on a more rigid beam path, so I wouldn't need to perform as many adjustments. If I had less time, I would most likely purchase an SLM, while if I had more time, I would work on driving the SLM from a microcontroller to reduce the footprint of the setup. I believe the setup could be reduced to a more manageable size.
  2. What have you noticed about your own mind, in the way that you create ideas, implement ideas, and test ideas? Consider both cognitive and emotional variables.
    I try to go for the path of least resistance when developing an idea--try the easiest elements first. Conversely, when planning an idea out from beginning to end, I like to focus on the most difficult elements, since they contribute the most likely modes of failure. I also like to have a fairly solid grasp of the theory, but I try not to get bogged down in minutia.
  3. What was the most important resource you now use, that you did not know about at the beginning of the term? How can you find more resources, more rapidly, in the future?
    Albert Mao's thesis was invaluable in the design of the project, and this helpful previous work shows that literature reviews can greatly accelerate a project if they find previous work that is similar to the proposed work.

Week 15 (5/14-5/17)

  1. What have you learned about working with others? Are there proactive or responsive things you should do differently, to maximize work with others?
    I've learned that working with others can be helpful for a project, especially when the team members abilities complement one another. It's important to set up tasks in a parallelizable fashion to minimize dead time for the group members. I also think that each group member should take proactive steps to make the corresponding group member adhere to strict schedules so that more work can be completed.
  2. If you had twice the resources to do the project, what would you differently? What about if you had half the resources? How does this thinking change your actual plans?
    If I had half the resources, I would need to devise a way to minimize the number of lenses used in the construction of the beam path, since the lenses are an expensive element. If I had twice the resources, I would most likely purchase a commercial SLM and perhaps commercial telescopes to minimize the construction time.
  3. Based upon your reflections of the previous week: are there things you can practice, to make you more efficient at creating, implementing, and testing ideas?
    I should practice making and meeting incremental milestones, as well as sticking to schedules I have previously planned out for myself. I can also practice identifying the significant components of designs that require works, since this is essential to developing quality ideas and testing them.