Stefanie Baker's blog

Sorry I didn’t get a chance to put a blog out last week, so I am combining the last 2 weeks into 1 final blog post. Throughout these past 2 weeks, I had to do a lot of analyzing and tying up of loose ends. I figured out the memory issues, figured out the extraction of the individual peaks to get the area under them, programmed labview to be more normalized from sample to sample, ran all of the collected data through the labview program, saved all the data, analyzed the data that was outputted further (made graphs and other sorts of things), and put together a final presentation.

This week I re-ran the phytoplankton cultures from beaver army terminal. The original samples that I took produced negative voltage readings—the entire signal was just shifted down into the negative range on the y-axis. I wasn’t sure if this was going to be okay, but as I looked at the other samples, I noticed that they all start at different y-axis levels. This data will still be good, however, because subtracting all of the amplitudes from a threshold will give the relative peak heights, which is what is important, not the amplitudes themselves.

This week, I began by running samples from the Beaver Army Terminal through the uFCM and compared it with FlowCAM as I ran it in connection with one another. I ran the uFCM at different sampling rates (5000k and 10000k) to try to resolve the peak definition. I also had to filter the water first with a 100um filter net so that the larger particles wouldn’t clog the uFCM flow cell. The first sample from the BAT was a bit old as it had been sitting in the cold room for a little over a week.

Monday: Today I did more LabVIEW programming. In the functions palette, I found a function called “Trigger and Gate.” After reading what this function did exactly, I programmed it to find the area under a specified peak instead of finding the area under the curve for the entire iteration. Once you specify a certain voltage amplitude for the program to trigger, it will do what you tell it to do for that trigger. In my case, I am telling it to trigger above a certain threshold, so that I will get the area under each peak that it triggers.

Monday: Today I ran the 5um beads with 5 drops of stock in 40 ml water (decreased concentration) on the uFCM. I also used a syringe pump instead of the peristaltic pump to try to get a more steady flow rate through the tubing in hope of producing a better signal. When running the samples with the syringe pump, the data was creating signals with a curved baseline. I couldn’t figure out what was causing it. This was the first time that I had used the uFCM by myself, so originally I had thought that I set up the program wrong. I also met Rachel Golda today.

This week I continued working with LabVIEW programming. I added more peak detectors with different threshold values. This way, I can program it to subtract between the different thresholds to get a more accurate count of the number of particles. As the program becomes more sophisticated, it will essentially replace the need to do any analyzing in excel. I also got the chance to run new samples through the uFCM. The 5 um and 20 um beads arrived and I made concentrations with 10 drops of bead stock in 40 ml of deionized water for each bead size.

Monday: Today I got the chance to take a trip to the Columbia River to collect samples by the Beaver Army Terminal near Longview, Washington. We also drove to Vancouver Lake to get samples from there. We left at 9am and got back around 1:30pm, so it was a nice little break from being stuck inside. Then I worked on my LabVIEW program. LabVIEW is on all of the computers in the lab now so I can start building my program without having to worry about which computer can handle what.

This week has gone by really fast and I am sure that the 8 more weeks I have here will be gone before I know it. My project has really picked up this past week. The computers in the lab had expired licenses of LabVIEW, so I couldn’t work on making the program for the beginning of the week, which was quite frustrating because all of the data that was processed using LabVIEW SignalExpress couldn’t be analyzed to the needed extent without having the normal LabVIEW software.

I had orientation on Monday 6/18/12 here at CMOP for my summer internship. We learned the basics of what CMOP does and some of the projects that they are involved with. This week was the “get acquainted” week where you learn everyone’s name, where their offices are, where their labs are located, the other buildings on campus, and other things of that nature. We also had safety training at the primate center (didn’t get to see any monkeys though), and got our ID badges.