X-ray CT of a Frozen Core From the 2009 Field Season
Ian, Dale and I spent yesterday afternoon and most of today together planning our field season, working on equipment, interpreting data from last year, and planning a future project to study Lake Untersee, also in Antarctica. Ian lives in the Solomon Islands, and Dale lives in New York, so it is very rare for us to work together in person. Usually, we communicate via e-mail or Skype. Working together in person is much more fun and productive.
One of the highlights was looking at some brand new x-ray computed tomography (CT) images of one of our frozen cores that we collected last year. X-ray imaging provides a map of density differences, so one can see how the dense minerals are distributed in the low density mat. Computed tomography is a technique for turning a whole bunch of x-rays into a 3D model of the density variations. I used a CT scanner in the UCDavis Center for Molecular and Genomic Imaging to image the core. This scanner is usually used to image mice, so my project was particularly novel and interesting to the staff at the center.
The imaging worked well. The calcite stands out very strongly in contrast to the ice and mat:
We spent more than an hour looking at the data in 3D in the KeckCAVES, a visualization facility that I help develop. We could highlight the calcite nicely:
However, when Ian, Dale and I tried to correlate subtle changes in gray to the mat and the ice, we had a very difficult time. We decided that we really need to cut the core and take a picture of it. I'll cut the core with a band saw, photograph it, and then match it to one of the CT slices (like that shown in the first picture). Hopefully, I'll be able to then see the boundary between the ice and the mat in the slice. Once I've identified that, I'll see what I can do with digital image processing to get those differences to stand out more. It will be a fun and difficult task!
Even though we weren't sure that we identified the exact boundaries between the calcite, mat and water, we learned a lot about how the calcite is distributed in the microbial structures. There is lots of variability, with sheets, columns, and rods of calcite, all connected differently. It will be really interesting to sort out all the variations. Tyler will have great fun with this!
We have 4 more cores to image, and we'll collect more when we go back out in the field. This is an exciting new technique to apply to these cores, one that will give us lots of insights into how the microbial structures grew!
One of the highlights was looking at some brand new x-ray computed tomography (CT) images of one of our frozen cores that we collected last year. X-ray imaging provides a map of density differences, so one can see how the dense minerals are distributed in the low density mat. Computed tomography is a technique for turning a whole bunch of x-rays into a 3D model of the density variations. I used a CT scanner in the UCDavis Center for Molecular and Genomic Imaging to image the core. This scanner is usually used to image mice, so my project was particularly novel and interesting to the staff at the center.
The imaging worked well. The calcite stands out very strongly in contrast to the ice and mat:
 |
| The circle is where the core is and the arch at the bottom is the core holder. The white parts are calcite and the gray parts are mat and ice. It is hard to tell the mat and the ice apart, and you can't in this image. |
We spent more than an hour looking at the data in 3D in the KeckCAVES, a visualization facility that I help develop. We could highlight the calcite nicely:
 |
| The calcite is approximately outlined by the various surfaces in this image. It has a very complicated distribution. We thought the "branch" on the upper right had broken off, but it is actually connected to the column that looks like it grew straight up. |
However, when Ian, Dale and I tried to correlate subtle changes in gray to the mat and the ice, we had a very difficult time. We decided that we really need to cut the core and take a picture of it. I'll cut the core with a band saw, photograph it, and then match it to one of the CT slices (like that shown in the first picture). Hopefully, I'll be able to then see the boundary between the ice and the mat in the slice. Once I've identified that, I'll see what I can do with digital image processing to get those differences to stand out more. It will be a fun and difficult task!
Even though we weren't sure that we identified the exact boundaries between the calcite, mat and water, we learned a lot about how the calcite is distributed in the microbial structures. There is lots of variability, with sheets, columns, and rods of calcite, all connected differently. It will be really interesting to sort out all the variations. Tyler will have great fun with this!
We have 4 more cores to image, and we'll collect more when we go back out in the field. This is an exciting new technique to apply to these cores, one that will give us lots of insights into how the microbial structures grew!
