Week 2: What's in the box?

By Lindsay Walker

This year the micropaleontology interns will dedicate most of their time to cleaning up unfinished projects from the previous two summers, working through the remaining quota of images and CT scans, and, finally, wrapping up with quality control checks. At the AMNH, each microfossil collection typically corresponds to a paper (published or unpublished), usually written in the mid-20th century or earlier. Part of what makes our work interesting is that every collection is different and, consequently, presents its own curation challenges. Below are descriptions of some of the projects we’ve been working on during our first two week at the museum.

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Dorr? (Year?)

No publication

Collection of foraminifera similar to those gathered by the H.M.S. Challenger Expedition (1873-1876)

Not every microfossil collection can be clearly associated with a publication, and sometimes specimen slides contain misleading information. For example, this week Brittney was assigned a collection that appeared to have been collected by the famous H.M.S. Challenger expedition, which led one of the earliest attempts to document marine life across the Atlantic, Pacific, and Indian Oceans. The resulting monograph was authored by Henry Brady (1884), a pioneer in the study of foraminifera, and is still widely used today for its high-quality illustrations. Needless to say, this collection was a potentially exciting find. Only after consulting our resident foram expert was it determined that the collection was actually made by an unknown collector--possibly "Dorr"--who may have revisited some of the Challenger's original collecting localities. Brittney has been matching specimens from this collection to their locality information, including forams from Fiji and Tonga (27 slides) and Sable Island (unquantified # of slides).

Route of the H.M.S. Challenger Expedition

Brady’s monograph contains detailed illustrations relative to most other publications the interns are working with (compare to Diamond 1928, shown below).

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Coryell & Cuskley (1934)

Some ostracodes from the “White Mound” section of the Haragan Shale, 

Murray County, Oklahoma

Description of lower Devonian ostracods published in American Museum Novitates 

Morgan’s first collection did not contain foraminifera, but was a large collection of ostracods collected by H. N. Coryell of Columbia University. The collection was partially completed by a former intern, but 40 slides remained to be curated, rehoused, and databased. Morgan was responsible for completing these tasks, as well as imaging one paratype to compliment the 16 previously imaged holotypes.

Paratype specimen Condacypris bindoa (AMNH-FI 103075)

Image by Morgan Black

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Diamond (1928)

Oligocene Foraminifera from Palma Real, Vera Cruz, Mexico

Unpublished thesis by Columbia University master’s student

The Diamond collection was Lindsay’s first project. It contains 45 slides of foraminifera, several of which may contain new species. This collection was completely uncurated when Lindsay received it, meaning she had to catalog, database, and rehouse every specimen present, as well as document any missing slides or lost specimens. All potential new species were imaged, and one of these specimens, Gaudryina n. sp., was added to the CT scanning queue. Because the results of this master’s thesis were unpublished, it is likely that these specimens have remained untouched in the museum’s cabinets for nearly a century.

Comparison of hand-illustrated specimens and a digitally imaged specimen from the Diamond thesis

Image at right by Lindsay Walker

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Kling (1960)
Permian fusilinids from Guatemala

Analysis of fusilinid foraminifera published in Journal of Paleontology

As the invert paleo interns learned from Ellen Thomas this week, fusilinids comprise a group of foraminifera that disappeared along with >90% of other marine species during the end-Permian mass extinction event (~250 Ma). These forams differ from other foraminifera in that they are much larger (visible to the unaided eye) and their tests (shells) are structurally more complex. This week Sam imaged and databased 40 petrographic thin sections from this collection of fusilinid foraminifera. That this collection contains only thin sections is unusual; most of the other AMNH microfossil collections consist of specimens glued to cardboard slides. This meant Sam had to image every slide in this collection as opposed to type specimens only, as is the standard protocol for collections mounted on cardboard slides.

Thin sections showing the cross-sectional views of fusilinid foraminifera

Images by Sam Martin

Week 1: Introducing the 2015 Intern Team

On Monday, June 22, the final group of paleontology interns arrived at the AMNH to help with the ongoing microfossil conservation and imaging project started in 2013. For our first week, we’ll be introducing ourselves as you’ll be hearing more about us in future blog entries.

Left to right: Claudia, Lindsay, Morgan (front), Brittney, and Sam will be helping complete the microfossil conservation and imaging project started in 2013. They hope the diversity of their past experiences will help them meet this challenge under the guidance of Bushra Hussaini, Senior Scientific Assistant in the Division of Paleontology.

Morgan Black is a current undergraduate student enrolled in a B.S. Geology degree program at Morehead State University. She has an emphasis in biogeosciences and is currently a palynology research fellow under Dr. Jennifer O'Keefe. Morgan is currently researching a set of fluvial/lacustrine deposits in eastern Kentucky and plans to present preliminary paleoecological data at the annual GSA meeting in Baltimore this fall. She was the only winner in the United States of the American Association of Stratigraphic Palynologists undergraduate award in the 2014-2015 academic year. She is very excited to be here at AMNH gaining more experience in the field of micropaleontology, along with databasing and computed tomography, and hopes to bring back much of what she learns here in the museum to her university.

Claudia Deeg, like the other interns, is not a New York City native, but is originally from Philadelphia. She is an upcoming junior at Smith College where she is working toward her undergraduate degree in biology with a minor in geology. At Smith, Claudia has been studying foraminifera spanning the Cretaceous-Paleogene extinction event under Dr. Sara Pruss. This is her first time working in a museum and Claudia is particularly looking forward to learning more about the technology used to image microfossils.

Sam Martin is a returning intern from 2013. Since then, he has graduated from Southern Illinois University with a honors B.S. Geology degree. He is now going into his second year of graduate school at East Carolina University where he is pursuing a master’s degree in Geological Sciences. His research as a graduate student continues to focus on foraminifera. His working thesis, entitled Distribution and taxonomy of modern benthic foraminifera of the Sunda Shelf (South China Sea) off peninsular Malaysia will, for the first time, document the foraminiferal assemblages and diversity present in the shallow waters of the western South China Sea. He is excited to take a break from his own thesis and help finish the microfossil conservation and imaging project he helped start two summers ago.

Brittney Oleniacz is a current master's student at the University of Kansas in Museum Studies with an emphasis in natural history. Her thesis focuses on the public understanding of natural history museums and the research they produce. During the academic year, she is employed by the KU Biodiversity Institute on a digitization project in the invertebrate paleontology collection. She is interested in understanding microfossil taxonomy, an unfamiliar group to her, and gaining more experience in digitizing museum collections, making them accessible worldwide.

Lindsay Walker is a recent graduate of the Museum and Field Studies M.S. program at the University of Colorado-Boulder. She worked with microfossils and fossil insects for her undergraduate and master’s theses, respectively, and her graduate program emphasized natural history collections management. Lindsay is looking forward to learning how to navigate the challenges of curating and conserving historic research collections. Because imaging has become an increasingly important facet of collections management, she is also excited to work with CT scan data, among other imaging techniques, while at the AMNH.

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.

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

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 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!

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!

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.