Spring 2012:Leanna Morinishi Journal

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20.345: Bioinstrumentation Project Lab

Leanna        Notebook        Lab I        Lab II        Final Project       20.345 Main        Sp12 Projects       

Week 15 - May 14-20


  • What have you learned about working with others? Are there proactive or responsive things you should do differently, to maximize work with others?

Oh, I'm definitely bad at initiating. I should be better at communication, promptness, doing things I'm not comfortable doing.

  • 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 resources = $$ I would straight up buy a microlens array and a camera. I think the optics of the Lytro hindered our progress (not as much as we hindered ourselves, of course)

  • 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?

Be more open to try to do things I've never done before.


  • Made agarose sample to try and get some depth. Unfortunately, the bead sample was not concentrated enough, I only found a few beads, very sparse. Will have to redo.
  • Instead took pictures of hair and onion skin! Looks interesting, can't really do anything beyond that since my Matlab just refuses to do anything.
  • Vincent did an overhaul. AN OVERHAUL. He tore apart the Lytro, removed the dichroic, the telescope, added a different light source and a diffuser, removed the diffuser.. From what I can tell, he cut out some shapes for a darkfield(?) scope in CSAIL and by hand. The man did some serious science.
  • I cleaned up. I feel redundant.

Week 14 - May 7-13


  • 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?

Twice, I'm not sure. I guess I would have actually attempted to write the hexagonal code. Torn up the Lytro. Half, I would have taken the Lytro, taken the images, and dealt with interference, etc.

  • 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 do not do well when I am sick, physically or emotionally. Personal issues definitely affect my work ethic. I can be a quick learner, I can do good work, but if my heart's not in it, quality tanks.

  • 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?

My friends. My god, they really helped me out. I didn't understand how to do command line anything. Now I can open terminal. And type things into it. And sometimes things happen.


  • Redid what Vincent tried to do. This time with more cage. Alignment, etc.
  • Changed scope a little. Tried a galilean telescope, a -35 non-aberration, a 250 tube lens (WAYY too much spherical aberration).
  • Added in a beam splitter so that we can use the CCD camera to focus the Lytro. Found a way to focus the camera at an appropriate distance so that we are able to see the magnified image as it exists in space in front of the lens.
  • Understand how to use terminal! Can split my images into .jpg stacks and/or .raw and/or .tifs!! This is a big step for a newbie like myself.
  • Matlab continues to give me the error: Undefined function or variable 'parforstart'.
    • Googling of problem gave me no answers. Exact same code runs fine on Vincent's laptop. Mystery unsolved. :(

Week 13 - Apr 30-May 6


  • What is the biggest thing you would have done differently in your project, given what you've learned throughout your project so far?

I really would have just bought a microlens array and a camera. I probably also would have tried harder. I would also not be a senior. Maybe a junior or sophomore.

  • 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?

Something small, with an interesting 3-dimensional structure. I think at our magnification that we could do neuron connectivity.

  • Reflect upon your pilot project from the previous week: did you carry it out? Why or why not?

No. Hexagons be hatin'.


  • We tried something different this week. a little expanding telescope. Kind of works, we can take pictures.

Week 12 - Apr 23-30


  • Is there any part of your project that you now realize is not so important, and should have been skipped?


  • 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)?

How to deal with a lens you know nothing about. That the internet does not, in fact, hold all knowledge.

  • 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.

Aww. This is a great idea, I'm a bad student.


  • Moved the microscope up a few inches, the alignment was not going to work with the given setup. Double mirrors should still allow laser to work.

Week 11 - Apr 16-22


  • List at least three statistical techniques you plan to use.
  • Generate simulated data sets and test these techniques.
  • What was the part of the project that you originally didn't think was important, but now has become a major task?

Getting the computer to understand our images. Hexagonal array.

Week 10 - Apr 9-15


  • 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.

LFDisplay, Dron, nrpatel-lfptools, any and all papers on this site.

  • What was the most fun part of your project so far?

Constructing the microscope.

  • What task are you procrastinating the most?

Answering these questions. For sure.

Apr 12

  • Tore apart, reassembed, featuring a telescope of -50mm lens, 125mm 2 in lens, 200mm 2in tube lens

Apr 10

  • Received lytro camera set up in thorlabs equipment
  • Took apart and reassembled bright/fluorescent microscope to fit the camera
  • Saw air force 8.0 on 8x zoom

Week 9 - Apr 2-8

  • What is the riskiest element of your project? What is your backup plan if that element fails?

Buying a product that we know nothing about.

  • List two skills you will have to learn in order to complete your project.

How to use terminal, how to determine NA, M, other relevant characteristics of lenses we know nothing about.

  • What companies make products related to your project? Whose products are the best?

Lytro makes this camera. Nobody else really makes something like this commercially. As far as components, it's possible to buy nicer cameras from allied vision technologies and a microlens array from edmund optics, thor labs, omron.

Week 8 - Mar 26-Apr 1


  • Did you enjoy spring break?

A little too much.

Week 7 - Mar 19-25


  • What is the most important thing you accomplished during the first week of your project?

Mostly realizing that we were going with a Lytro camera instead of purchasing a microlens array and new camera.

  • What three things do you plan to accomplish in the next week?

It'd be nice to get the bright field and fluorescent microscope going.

  • What three things do you plan to accomplish in the next month?

Get an image and process it with our materials available, determine what actual code we need to do.

Mar 20

  • 3d experimental psf image acquired! See Lab 2 for more details.
  • 3d theoretical psf image acquired! You need to be sure to make the type of the image 8-bit.

Week 6 - Mar 11-18

Mar 18

  • Steve helped us tremendously in figuring out what to do with the f*cking camera and dealing with its poser object oriented code
  • Celebrate! the microstepper is installed on the stage
  • Microstepper steps
  • Took an image stack of psf beads
  • Did some stuff to help out with the sleep mode. Controls to come shortly...
  • AJ to GUI design tonight, hopefully we'll get a nice 3d image of our psf by tomorrow!

Mar 17

  • Changed the step function to digital output 1.1. Now our 5 digital outputs are [Direction STEP M1 M2 M3].
  • Code now:
    • walks half distance in one direction
    • walks full distance scan taking a photo at each point
    • walks half distance back to original position
  • Distance for zresolution calculated using the Nyquist Calculator[1]
  • Simplified breadboard.
    • Consolidated wires
    • Removed voltage divider, as we are now driving the entire circuit with the 5V output generated by the pololu driver itself.
    • Consolidated grounds
  • Checked fluorescent distribution, looks pretty good, could probably be better.

Mar 16

  • Worked on getting matlab talking with the camera.
    • Activated Matlab adaptor, explored camera attributes.
  • Took a photo.

Mar 15

  • Met the microstepper and its associated code!
  • Looked at the electronics, and fixed up the wires a bit.
    • Steve helped me find the culprit of the buggyness: a wire giving _enable_ some data. We really want _enable_ at zero.
  • Added microstep controls on the digital output of the DAQ.

Mar 13

  • Proposal, Porposal, Poporsla

Week 5 - Mar 4-10

Mar 6

  • Wrapping up the Lab I report with more calculated $ l_p $ and $ l_c $ values, and more centering proof. Maybe even some better gui pics.

Mar 5

  • Working on the wiki. Put in a simple navbar, reorganization. Did some literature searching, and started my objectives for the final project. Will be working with AJ and Vincent on Lab II.

Week 4 - Feb 26-Mar 3

Mar 2

  • BIG MANUPS got the code to actually work. After thinking and talking with Steve about what voltage to subtract and where, the stage finally moves towards the center after 1 cycle in each direction, given that the amplitude is large enough to see the entirety of the bead. (using 3 micron stuck bead samples, no tethers yet. Theoretically should work the same.)
  • The new equation now looks like
    • handles.CenterPositionY = handles.CenterPositionY + BinnedData(centeredPositionIndexY, 4)-currentPositionY;
  • Made 3 micron sample. The dilutions that have been sitting out at room temp don't seem to be too happy. It's probably best to re-dilute and re-make the sample.

Mar 1

Feb 28

  • Got integration working, Also, the stage is moving nicely, we are currently using 3 sinusoidal cycles, but for the sake of the tether, we will begin to cut this down to 1 in each direction.
  • Tested with stuck beads, since it gives a decent curve if the trap is focused at the correct plane.
    • 3 micron beads work great, large enough to detect
    • 7 micron beads are just too damn big. They just are. Don't use them.
  • Switched gears a bit so that we no longer invoke piezos, we give a voltage and redefine a new UiSettings attribute in each round.

Week 3 - Feb 19-25

Feb 25

  • Integrated with OTKB and tried to open communication with GUI, it's a start, but there were many bugs to fix, mostly involving capitalization and the calculation of NumberOfSamples to collect with regards to the SampleRate.

Feb 24

  • Combined AJ's piezo directing function with my centering function. We are still deciding between the max-min ==> center method or the derivative method for finding the tether center location best.

Feb 23

  • Met with AJ, decided to pair up, shared code

Feb 20

  • 3pm Moved some voltage through the DAQ today. Worked on understanding time, SampleRate, SamplesPerTrigger, TriggerRepeat, RepeatOutput, establishing channels, starting and stopping data output and input.

Feb 19

  • I'm Leanna, a senior in Course 20. I find all sorts of things fascinating which is both a joy and a nuisance. Through 309, I began to better understand the impact of improved imaging tools on fundamental movements in the field, and I would love to broaden this learning experience to at least 3 new imaging- or measurement- related approaches this term. As a scientist, I really feel like I need to better understand not just the function of the scopes available commercially, but also the physical concepts and limitations associated with them. Specifically I'd like to learn more about image processing and/or 3D imaging. I think it would be great to be able to track cell migration or other small movements in 3 dimensions over time with the parts available to us in the 309 lab. Light field microscopes are also pretty cool. :p
  • In lab I, I hope to come to understand the basics of data acquisition. Programming/MATLAB isn't my strong suit, but I'd love to learn more.
    • Complete a button that takes in data from a tethered microbead and adjusts the stage position to center it on the tether
      • Try to get nicer calibration data
      • Function that finds the center
      • Feed in recorded data in a simulation
    • Look at the properties of the tether, to calculate the persistence and contour lengths

Week 2 - Feb 12-18

Feb 17

  • Wrote some preliminary center-calculating code, using the data obtained on the 13th. This function bins the data from the QPD by the strain gauge voltages, and then uses the maximum and minimum voltages of this binned data as the edges of the trap and takes the median index to find the "center" of the trap in that direction.

Feb 15

  • 1.30pm DNA Tether Prep with Marie's leftover materials, Steve found a few attached beads on his samples, I found one.
  • They didn't move so well, and I didn't have code going yet, so we didn't test anything beyond OTKB and beginning to understand its syntax.

Feb 13

  • 12pm Walkthrough of OTKB software and took some great calibration data at 20mW 70mW and 120mW of .97 micron beads.
    • This is the data I used for the proof of principle for the center-finding function.

Week 1 - Feb 6-11


  1. NyquistCalculator