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: www.tmrives.com
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: www.amnh.org

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

Monday, July 28, 2014

Interlude: CT Scanning Microfossils


CT-Scanning Process
One aspect of our work this summer is creating 3D images of some of our specimens. This can be accomplished non-destructively with the CT (Computed Tomography) scanner down the hallway in the Micro-Imaging Facility.
GE Phoenix Vtomexs
GE Phoenix CT-Scanner (photo credit: http://research.amnh.org/mif/node/12)
Before we scan a specimen, we mount it in the tip of a micropipette and place it inside the CT-scanner. The specimen is mounted between an x-ray source, which shoots x-rays at the sample, and a detector. Much like a camera, which creates an image based on how much light enters through a lens, the CT-scanner creates images based on how many x-rays reach a detector. Dark spots in the image mean that x-rays traveled directly from source to detector; brighter spots appear where the x-rays passed through denser materials.
AMNH-FI-87587 Uvigerina strata
To obtain a 3D image, the x-ray source remains stationary while the sample rotates. While the specimen rotates, the scanner gathers data at set intervals, ultimately producing more than a thousand images. This process can take anywhere between 30 minutes and 2 hours. At the end of the scan, we transfer the raw data (over a thousand high-quality images and other proprietary files) onto a hard drive. While the CT scanner's job is now complete, the intern's work is never over.

CT-Scan Processing

Cleaning up a CT scan and sectioning it

We use software created by the scanner's manufacturer to reconstruct a volume from a series of 2D images. Then, we edit this volume in VG Studio. Because the mounting materials are denser than air, there is usually unwanted noise in the scan. Sometimes removing all of this noise to isolate the fossil can be a very time-consuming process.
Region Growing in VG Studio
After isolating the specimen, we create videos and interactive files showing internal and external 3D structure. We can even send our processed CT scan data to one of the museum's 3D printers! 
gif of the CT scan of AMNH-FI 87934 Cibicides fletcheri


A 3D-printed Foram!



Friday, July 25, 2014

Week 5

Collections tour

Materials used for the preservation of AMNH's giant squid

This week's collections tour led us through the Invertebrate Zoology department. Their collections manager gave a spirited tour of the vast and diverse collection. Some highlights included enormous scarab beetles, bedbugs, butterflies, a deep-sea isopod, and a giant squid! We even got to touch one of the squid's tentacles. After which, we agreed that we will never again voluntarily touch a giant squid tentacle. It's convenient that they are elusive creatures!

Another highlight of the tour was seeing Alfred Kinsey's collection of 7.5 million gall wasp specimens. That's right: Alfred Kinsey, of Kinsey Report fame. It turns out that the iconic American sex researcher began his career researching gall wasps, and that his immense collection is now housed at AMNH.

As we do in most of our tours, we also talked about problems in collections management. Like in many other biological collections, dermestid beetles are a problem in the dry invertebrate zoology collections. Because the anti-pest chemicals previously used in AMNH collections were discontinued for potential safety issues, collections managers have recently needed to find new ways to deal with pests in their collections. Another issue, in the alcohol collections, is evaporation. Rubber seals on old jars often degrade, allowing for alcohol to rapidly evaporate, leaving samples desiccated.

Continuing with the Warthin Project

Work Desk
Four of us were working on the Warthin project this week. As was mentioned in last week's blog, over 500 additional specimens were found in the old collections and need to be added to a project that was started last year.

Assigning new AMNH numbers







We organized the specimens from each original box, alphabetizing and rehousing the slides.We also assigned new AMNH catalog numbers to each slide and entered information listed on each slide into the Panorama database. Next week Courtney will compile all of the slides that were processed and organize them for long term storage.




Digging for Information 

Researchers dug these fossils out of the ground years ago, but us collections interns still have some "digging" of our own to do. Many of the collections we're working with have been disassociated from their original publications. Finding the publications in which species were originally described has been a very interesting part of this project, from an institutional history standpoint. Sometimes it's like solving a mystery!

Some collections have original correspondence associated with them which helps to understand how to curate the specimens. It's fascinating to read historic typewritten correspondence between researchers and museum curators. Many of these letters include information about exactly which specimens were sent to the museum, what paper they were published in, and why they were sent.

Another obstacle in researching our specimens is language! Interns this year have worked with papers in German, Italian, Spanish, and Dutch. Thankfully, our scientific consultant, Ellen Thomas, is a polyglot. She has been able to help us out when language gets in the way of understanding how to organize and catalog our specimens.

Preserving these collections as historical artifacts as well as scientific specimens is a large part of our work. We catalog these fossils as they are originally published, even if their species names have been revised since then. From a historic standpoint, it has been fascinating to see the changes in scientific methods and publications over time.

As you read, it's been another busy week in the microfossil collections. We'll be back soon with more exciting news and information!

Wednesday, July 16, 2014

Week 4

Locating Publications in the Research Library

Many of the projects we have worked on are associated with at least one published paper (or in some cases Columbia University masters thesis papers). It is our to job to locate additional publications that use our specimens and make note of them in the database.
Most times we can find  publications online using the electronic resources that are available to us, but sometimes the publications are only available in print at the research library. Luckily for us the library is just downstairs from our lab.


Large collaborative effort ahead

This week we wrapped up some of our smaller projects and are moving on to one larger task.

Courtney worked on the project on her own last summer and cataloged over 500 specimens. At the end of the summer it was assumed that the project was completed, but we have located 8(!) more original storage boxes that are directly related to a publication by A.S. Warthin (1930). Each of the original boxes can hold up to 100 vertical slides.
original condition of the Warthin collection
In addition to the sheer number of slides, each slide holds an unknown number of specimens. Many of the slides are missing their specimens because they were housed without cover-slips. We need to properly store the slides to prevent further deterioration of the specimens and to assign catalog numbers so that they can be added to the fossil invertebrates database. Some of the specimens are types and will need to be photographed. We have our work cut out for us next week but we are up to the challenge.

Ostracods of the Week

We proudly present to you the ostracods of the week.
Cavellina fittsi paratypes from a 1929 Columbia Masters' Thesis
Rebecca takes full credit for the superior aesthetics of this image, which required extensive rearranging in Photoshop. You can see a wide variety in the size of specimens here. Ostracods are arthropods (like lobsters and ants), so they grow in a fixed number of growth stages, or instars. This can make it difficult to classify ostracods, because different instars of the same species can be mistaken for separate species. 


Collections tour

 This week we had a tour of the ornithology department's collection.

 Nicollette even got to hold a bald eagle.

We have reached the halfway point of this project. It seems as though we started just a few days ago and we still have much to learn about updating collections.

Until next time,
The IP-microfossils team.

Thursday, July 10, 2014

Interlude: Why are microfossils important? What are these things?

Most people think of huge dinosaurs and mammoths when they think of paleontology, not tiny one-celled organisms with a calcite "test" (like a shell), or miniature crustaceans that can only be seen under a microscope. While these microscopic fossils may seem less exciting than a dinosaur or an ancient fish, they actually are in many ways more important to the paleontologist's quest to chronicle the history of life on earth. These tiny animals incorporate carbon in their tests and inadvertently preserve information about a host of environmental conditions while they are alive. When interpreted by paleogeochemists, the tests of foraminifers can be used to extract information about temperature, salinity, and facies changes. Their tests, while beautiful, are also quite useful in informing us of change on geological time scales. Similarly, the shells of ostracods are used in paleoclimate studies.

In addition to being useful for paleoclimate reconstruction, microfossils have been useful in industrial settings as indicator fossils. Because many species are short lived and environment specific, paleontologists use them to determine the geological age and environment in which the foram was deposited. Oil companies often employ paleontologists to determine when an oil bearing rock layer has been reached. Because of this industrial use for forams, many of the collections we are working with were collected as part of oil drilling operations. More about forams from UCMP

Extant analogs

Some of the organisms we encounter in the invertebrate paleontology lab have extant analogs that are studied by ecologists. Knowledge of habitats and behavior of certain genera in modern settings can help us to interpret the fossil record. Here are some videos that show some of the animals that are in the invertebrate fossil collections .

Live Ostracods

Video credit: nymdevente (youtube user)

Live Foram feeding

Video credit: foraminiferal (youtube user)

What are we contributing?

This conservation and rehousing project will make the microfossil collections of the American Museum of Natural History more easily accessible to researchers and the general public. Of over 7,000 specimen lots in the AMNH microfossil collections, most specimens are types. By photographing type specimens, we are making it possible for researchers to see images of specimens before they decide to come to the museum in person.

Before this project started, many specimens were difficult to locate in their storage spaces at the museum. We are ensuring that specimens are correctly associated with the publications that describe them, and that their storage location and other important data are entered in an electronic database.

Another important part of this project is rehousing the specimens. Many older slides were housed vertically, allowing for fossils to fall out of the slides when the adhesive holding them in place decayed. We are rehousing slides in metal holders with glass cover slips. The slides are then stored horizontally in boxes according to the publication they are associated with.
Work desk. At left is an original wooden slide box.

Specimens in their new home.
Hopefully, our efforts will contribute to the creation of an accessible collection for the use of researchers and microfossil enthusiasts around the world.

We hope this interlude helped you understand the fossils we work with and the importance of this project. Look forward to our next weekly update: The Adventures of Week 4.


Wednesday, July 9, 2014

Week 3: The Saga Continues

Hello again,
It's business as usual for the microfossils interns. Here is a recap of our week.



Week three was short and sweet due to the national holiday, but we still managed to get a lot done.
We assigned over 300 new AMNH catalog numbers. Some of us also got to do CT scan reconstructions in preparation for the samples we will be running next week.
Hard at work on the database

Disasters arise!

Sometimes the microfossils get away! Many items in our collection are from research projects that were done almost a century ago. Glue and tape begin to break down over time, so we must rehouse our material on new slides. Even with the lightest touch we are in danger of breaking fragile samples or having a sample 'jump' off of its original slide. When that happens, we do our best to recover our fallen comrades.


Shaun assisting in the recovery of an ostracod

Dustracod sighting

Sometimes samples that were thought to be missing are recovered near the working area or in the original box. We do our best to keep our collection as complete as possible.


In our attempts to locate ostracods, we stumbled upon a strange and interesting specimen.
"Dustracod"? "Dustram"? What are you?



At first we thought the specimen to be a foram or a lost specimen from last year's intern. It turns out it was just a spec of dust or perhaps a mineral from other researchers who visit our lab.
We thus named the "specimen" the dustracod and continued our search. We have yet to locate our slippery holotype.

WOW! Look at that photogenic fossil!

Here is a photo of a nummulite Kat photographed this week. There is evidence of the beginnings of pyritization - or pyrite decay - in this specimen.

A nummulite undergoing pyritization



A close up of the pyritized section

See? The mineral pyrite is forming in certain areas of the fossil. There is also a fine white dust seen in the cracks of the fossil. Though this may look like the matrix the fossil was found in, it is actually an early stage of pyrite decay. Unfortunately, this means that the fossil is in a state of degradation, and will soon be unable to use, unless something is done. Our rehousing project is a preventative action against this development, as one of the main reasons that pyrite decay occurs is because of increased humidity.

Tour of the Week

This week we visited the Icthyology department with Rad Arindell. We saw how they obtained and preverved specimens for their dried and alcohol collections. As a bonus we also got to see the famous "living fossil fish" Coelacanth.

That's a lot of alcohol!




The saga of microfossil digitization continues...
Until next time
-Ipmicrofossils team