Taking the LiDAR out for a spin
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We took the LiDAR out for a spin on Friday. We had a beautiful (read: high tech) rig that consisted of Neil driving, Kellan holding the LiDAR out the sunroof, and Nic spread out across that back seat with the drone (Kia), laptop, and router, collecting data from the LiDAR. We re-learned that Kia doesn’t like having a lot of metal around, so our plan to collect GPS data was challenged, more on why GPS data is important below.

This is us trying to get a good GPS signal on Kia, not us actually driving with Kia sitting on the roof…
Note: Kia is the drone not that we are in a KIA car

 

 

After a lot of indoors practice with the LiDAR, we determined that the best way to set up Kia when in Iceland is to have a balanced rig with weight evenly distributed to the sides. The elements that we have to consider are the LiDAR, a wifi transmitter as well as battery packs for both. Neil and Charlie are working on getting these built in a reliable prototype.

 

Our ultimate goal is to create point clouds from the LiDAR data based on GPS coordinates. During our test run on Friday we collected data but are still mapping this data based on time instead of GPS. Our plans for Monday are to pull the GPS data from our Friday test run from the Kia and align the GPS/telemetry data with the LiDAR data in a point cloud. This will allow us to correctly map the data in a point cloud. We can’t map the LiDAR data using time because the LiDAR spins faster than our time readings and time is linear and our flight most likely won’t be linear. If we were to create the point cloud using time, we would have a straight line where the data would be stretched out and repeated.

The next generation of next generation sequencers has arrived!
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We have received, from Oxford Nanopore, the MinION. (Min-ION, not one-eyed yellow minions, get it straight.) This device promises whole-genome sequencing of microbes, viruses and archaea from soil samples we will collect at the Solheimajokull glacier. This device is extremely small and portable, and one sequencing run can be done on a laptop in 6-8 hours. One flow cell can run up to 12 samples at a time, and while the samples are being sequenced, internet access will allow simultaneous queries of a database that will determine what species were in our sample. Thus, in REAL TIME, we can identify the composition of the soil microbiome. This is a drastic improvement over prior methods, which involved sending 16s rRNA samples to a company and waiting for 2-3 weeks for results. 

What kind of science are we doing with this device?

We will be collecting soil samples at the Solheimajokull glacier (near the town of Vik in Iceland). We want to obtain samples that have been “out of the freezer” i.e. not covered by the glacier for a specific number of years – 10, 20, 50, 75, 100, 150, 200, etc. We will compare the microbial populations present in these different soil samples and look at the type of soil and flora growing in these different locations. This will teach us how the land “recovers” once it is freed from a glacier.

This device will help us do this analysis on site and give us the data almost immediately. It’s really new, cool and exciting. We’re looking forward to learning about soil succession with the use of this device!

 

Blogger: Emi (Biology Professor and MinION hand modeler)

Driving, of a sort
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This is the first of a couple of short clips from the GoPro dashboard cam that we used in 2016 (we plan to again this year). The wheat-to-chaff ratio is pretty low, but the kernels you do find tend to be gems. In this clip we are driving down to the red sand beach on the West coast of Iceland. It’s near the end of a long day of driving from Akureyri, Nic is at the wheel with “support” from Erin, Deeksha, and the Talking Heads.

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