Saturday, August 9, 2014

The Final Days

With less than a week left, we are scrambling to tie up loose ends and put everything in order for next
year's interns. This entails rechecking each project that we worked on this summer, making sure specimen documentation is complete and easy-to-understand, organizing our digital data (pictures, CT scans, database entries), and updating instructional materials for future workers.

This Week's Tour 

As a break from frantically organizing our microfossils, four of us got to hang out with Julie Feinstein and Alana Gishlick in the frozen tissue collections for our weekly tour.

The Ambrose Monell Cryo Collection (AMCC) is hidden away in the museum's labyrinthine basement. To reach it, we walked through the carpentry and metalworking departments. Next to an open-air loading dock, we found the AMCC's unassuming entrance. Once inside, we were greeted by the AMCC's collection manager, Julie Feinstein, in a small room that resembled a dentist's waiting room. Unlike a dentist's waiting room, however, there is a window in one of the walls that looks in on several enormous liquid nitrogen-cooled vats. 

Juile showing us how the tissues are stored
At about ten years old, the AMCC is the museum's newest collection. The AMCC stores samples of frozen animal tissues in tiny vials. Researchers extract DNA from these samples to study evolutionary relationships. Just one vial, with a capacity of a few milliliters, contains enough genetic material for a lifetime of research.

Because of the nature of the collections, the cryogenic collections space is kept completely sterile. Their facilities are state-of-the-art; samples are stored in trays inside passively cooled liquid nitrogen tanks. The liquid nitrogen comes in through specialized high-pressure insulated pipes, maintaining a constant level of liquid nitrogen in the tanks. Without the specialized pipes, the extremely cold liquid nitrogen could expand and cause an explosion. They are filled to about mid-calf height with liquid nitrogen, but the tank stays below -150 degrees Celsius because of the cold nitrogen gas filling the rest of the tank.

Even the filing system in the frozen tissue collection is high-tech. Each specimen vial has a barcode that, when scanned, brings up the sample's electronic database entry. It's a completely different world from portions of the invertebrate paleontology collections, where we worked to revise much older organization strategies.
Alana peering into the Liquid nitrogen vats
We were invited to look into one of the vats (with protective eye gear, of course) to see the storage conditions of the specimens and ogle at the boiling nitrogen. The nitrogen vapor cascades over the sides of the vat because it is heavier than the air in the room. It was an unforgettable experience!

Fossil of the Week

Polymorphina torta: photomicrograph on the left and CT scan in GLC_player on the right

We have chosen this foram because of its awesome internal structure. It also resembles a spaceship/a twisted leaf/a fish and is aesthetically pleasing to us. Rebecca discovered this as she was post-processing CT data this week. There is more to this foram than meets the eye! Note the difference between the photomicrograph and CT scan image. We experimented with a free 3D viewing program, GLC player, this week. The results were impressive, as you can see in the beautiful 3D image above.

The Summer in Review

Over the last eight weeks, we made 3,015 entries in the electronic database, took over 350 images of type specimens, and CT-scanned more than 30 microfossils. It's been a productive summer, and we all have high hopes for the future of this project. Thanks to everyone who made this possible: the National Science Foundation, AMNH, Bushra Hussaini, Lindsay Jurgielewicz, Alana Gishlick, Ruth O'Leary, Neil Landman, and the staff of the micro-imaging facility!
Alana and the Interns: An Up-and-Coming Girl Band
Finally, we want to thank YOU, our readers, for following this summer's adventures in microfossil curation. Come back next year for further updates on AMNH's microfossil rehousing and digitization project.

Friday, August 8, 2014

Week 6

Developments in 3D Presentation!

This week we experimented with making 3-D animations of our CT scans using VG Studio. It was a collaborative effort that resulted in several experimental videos and .gif animations, so we decided to dedicate a post to our discoveries.

Tour of the Week

We had a short tour of the Earth and Planetary Sciences (EPS) mineral collections and the electron microprobe lab. The EPS collections manager showed us some of their most interesting and attractive specimens. Many of their specimens are rare minerals or more common ones with unusual variations in composition. Some of us got to hold a huge "subway garnet" that was found under Manhattan during the construction of New York's sewer system.
The Subway Garnet. Photo credit:
Much like the invertebrate paleontology department, the collections staff in the EPS department are working on a large scale digitization project. We met their intern, who has been photographing minerals for an electronic database all summer. Because their collection is much smaller than the microfossil collection (in terms of total number of specimens), they have been able to photograph most of their specimens this summer.

The EPS department conducts a wide variety of research, from experimental petrology to meteoritics to mineralogy. While the work of EPS researchers and collections staff does not always overlap, they do work together to find specimens to use as standards for the electron microprobe. The microprobe needs to verify its element analyses with minerals with known compositions; minerals from the collection are perfect for this because they have already been characterized, and many contain rare elements.

Dr. Juliane Gross, a scientist in the EPS department, showed us the electron microprobe lab. Using this complex (and very expensive!) instrument, researchers obtain precise mineral composition data and create element maps of samples. The lab's most recent acquisition is a brand new carbon coater, which applies an extremely thin and even coat of nonconductive carbon to samples before analyzing them with the electron microprobe. This process ensures that the sample itself will not become negatively charged when exposed to the electron beam. As most of us interns have backgrounds in geology, we especially enjoyed this tour.
The Electron Microprobe Lab. Photo credit:

State of the Project Address

So far, we have made approximately 2000 entries in the electronic database. Many slides have multiple fossils on them, so the total number of specimens is over 6000! This week, we also spent time standardizing our method for saving and backing up CT scan data on our computers, server, and external drives. This will ensure that the data is not lost, and that next year's interns can follow a specific protocol for organizing their CT scan files.

Foram of the Week

Shaun photographed a beautiful foram this week. The gold sheen is not natural; we dipped it in gold so that we could have an artsy photoshoot with it. Just kidding! Actually, this foram is coated in gold for a purpose: to make it suitable for scanning electron microscope (SEM) imaging. Because the minerals that make up the sample are not electrically conductive, a conductive coating must be applied before SEM analysis.

Another feature of this foram is that you can see the recrystallized interior where the last chamber is broken off at the top. This was helpful for us when choosing specimens for CT scanning. Although the exterior is very well preserved, the recrystallized interior means that we would be unable to see detailed internal structure in a 3D scan. 

It's been another productive week for the invertebrate paleontology interns, and we hope that the next week will be just as fruitful as we approach the end of the internship. 

Until next time,
The Microfossil Team