Spring 2012:Leanna Morinishi Journal

Week 7 - Mar 19-26

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
• 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

• Wrote code to sort tether data into a force-displacement curve and used nlinfit to determine contour and persistence lengths.
• Calculate persistence and contour lengths by nlinfit
• Force Function for nlinfit
• Learned to use the Status function for EVERYTHING.

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

References