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Becoming more familiar with running the uFCM (Week 5)

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. She works in Needoba’s lab as well, but has been gone in Hawaii for an academic program. She worked a bit with the uFCM back in May before she went to Hawaii, so she has some background with the uFCM. To try to fix the curved signal, we placed aluminum foil around the uFCM to shield it from any excess electrical output from other instruments—such as the syringe pump. Doing this worked! I guess my settings were correct after all and the uFCM was just picking up other signals.

Vanessa Green took the interns and some of the high school interns on a day trip to Astoria today. We went to M.E.R.T.S. (Marine and Environmental Research and Training Station) at Clatsop Community College where we met with others from CMOP and they gave us a tour and some information about what type of work they do. They mostly deal with the building and managing of the underwater sensors and gliders. We then went to “the column” where there is a nice viewing tower that you can climb to get a good view of the Columbia River. After that, we went to the Maritime Museum and on the way back to CMOP, stopped by the house where the movie, The Goonies, was filmed.

This morning, I went with Estefania to the Beaver Army Terminal to collect more samples. Upon arriving back at CMOP, I filtered some of the water that was collected yesterday in Astoria with a 110 um filter so that it wouldn’t clog the flow cell in the uFCM. Marc and I also connected the FlowCAM in line with the uFCM so that it would be one continuous system and measurements could be better compared if the exact same sample ran through both machines simultaneously. I got worried that using a sampling frequency of 10,000, while good for detecting every particle, would fail in excel. I can only import about 1 million data points and a lot of the data is being cut out because it doesn’t fit into excel. So when I go to sort through it and perform analysis on it, I am only getting a few select peaks and a whole bunch of noise data, which is not useful.

Today I started looking at the data that had been processed through SignalExpress earlier this week. LabVIEW was having memory issues today—technical difficulties! When I try to export the data into excel, I receive a memory error and then the computer won’t let me close out of the program. I then moved on to running the phytoplankton cultures. I put the phytoplankton (T. Rotula, T. Pseudonana, T. Weissflogii) in new media because it was too concentrated. When running this through the FlowCAM, a lot of dirt was being detected, so I decided to discard that data and use a more recent culture that didn’t need to be diluted since it was newer. I ran the phytoplankton cultures in a continuous system with the FlowCAM. The FlowCAM pumps with a flow rate of about 0.31 ml per minute. With the extra tubing connecting the FlowCAM with the uFCM, it took about a half an hour to run 1 sample through. I also used 2 different sampling rates along with 2 different buffers for data collection. I sampled at 5,000 per second and at 10,000 per second. Some of the smaller phytoplankton had tons of cells in the sample, so reducing the sampling rate would help the system from crashing/stop logging data due to there being too much.

This morning I tried to figure out the memory issues that the computer has been having. I think that the best solution is to buy an external hard drive (1 TB) and save the data onto that. The interns also had another Brown Bag seminar today with Investigator Dr. Tawnya Peterson—“Issues facing women, men, and families in academic positions”. We learned about the different challenges that people face in science as they go through school and into the later years of their life along with how those challenges can be overcome. In the afternoon, I worked with LabVIEW and had my program read the phytoplankton data. I am still trying to decide how accurate the peak detector is in LabVIEW in relation to our data. Using LabVIEW only will solve the memory issues, but you can’t do that until the LabVIEW program is sophisticated enough to the point where it does all of the analyzing that you need it to perform.

Plans for this weekend…..
This weekend, I am going to go on a native pictograph (rock painting) and petroglyph (rock carving) tour at the Columbia Hills State Park. Some of my family is also coming to visit this weekend, which I haven’t seen in a while.I am looking forward to it!