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.

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.

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

Week 2!

Hello Again!
We are entering our third week of the microfossils project and are gearing up for a foram and ostracod filled summer! Here is a recap of what we have been up to:

Our first week was all about getting acclimated to the process of cataloging and entering information into the AMNH fossils database. (See our previous blog for more details about our first week and to get to know the 6 interns.) We also had to adjust to being at the museum, which is a lot bigger than one would expect. We work on one of the longest hallways in the city which stretches from Columbus Avenue to Central Park West!

The Invertebrates hall way...

Needless to say, getting lost in the museum was a regular occurrence over our first few days. By the end of the week we were officially registered as interns of the AMNH.

Trial and Error!

While week one was about getting acclimated, week two was all about trial and error.  It’s a challenge to make sure that all six of us are following the same protocols, but as problems arise, we quickly develop effective solutions. We have been using our experiences to update the guidebook that will outline the most effective process of cataloging the microfossils collection in the future. 

We have had a few hiccups, but altogether we were able to rehouse and catalog over 400 unique specimens this week! We each worked on one or two projects and spent time entering information into the fossils database as well as taking photomicrographs.

Rebecca working hard on the database

As a part of this project, we have also been using the CT-scanner to make 3-dimensional reconstructions of some of our most pristine samples. With help from the lab manager, we generally scan the samples for 1.5hr intervals. Then, final reconstruction and creation of working images varies from sample to sample. We haven't yet figured out how to make the final 3D PDFs accessible to the public, but hopefully we will find a way to include these in an online database.

In other news...

Nicollette thinks this Ostracod is especially photogenic and has nominated it to be microfossil of the week. As there are no contenders and we are still  processing our first few photographs, this week's fossil of choice will be Healdia gillae.

A photogenic ostracod

All in all it's been a busy week

Until next time,
The microfossils team.

A Warm Welcome to the Wonderful World of Microfossils! Week 1

Hello, blogosphere!


This year's crew of NSF-funded microfossil collections interns would like to take a minute to introduce ourselves before diving into the nitty-gritty of our first week on the job. We will regularly update this blog throughout the summer, as we work our way through revitalizing AMNH's long-neglected microfossil collections.


Now, meet the team:

Courtney is a graduate student at Western Illinois University pursuing a degree in museum studies. This is her second summer working on the Invertebrate Paleontology rehousing project and is excited to be back. She will be returning to the Midwest after this summer to start an internship at the Henry Doorly Zoo in Omaha, NE. After graduating she is hoping to work in natural history collections and is looking forward to what the future holds.

Nicollette is a Bronx native who is no stranger to invertebrate life forms.  While she studied geology at Oberlin College, she had the fortune of studying bivalves, gastropods, and even fire ants. Becuase she has never studied invertbrates that can't be seen with the naked eye, Nicollette looks forward to working in the microfossil lab this summer. Nicollette is especially interested in applying the fossil record to the study of paleoclimate and change over time. She loves the intersection of science and society and hopes to be a part of the discussion of climate change in the future. This fall, she will begin her Masters in geoscience at the University of Arizona (Bear down!).

Katherine (Kat) is a rising senior at Mount Holyoke College, currently studying Geology and English, as well as performing with the Mount Holyoke Symphony orchestra as principal cellist. She is from Laguna Niguel, California - a small town in Orange County - and is excited to get the feel of living in a real city. From the age of 5, she has wanted to be a paleontologist, and her passion for fossils hasn't wavered since. She hopes that the AMNH microfossil internship will bring her one step closer to her goal of being part of a vertebrate fossil prep team.

Shaun recently graduated with a B.S. in Geology from University of Houston and has a strong passion for geology and computers. He has also been working on georeferencing collection data to modernize the museum's databases. He is originally from Houston, TX.

Farallon is very happy to be a part of the microfossil intern team. Next fall she will be going into her third year in the College of Creative Studies at UC Santa Barbara, where she also does research on apicomplexan octopus parasites in the Kuris Lab. She is from New York City, where she lives with her family and four cats.

Rebecca just graduated from Oberlin College, where she studied geology (officially) and a smattering of other subjects, including Javanese music. Originally from Downingtown, PA, Rebecca is excited to explore the "real world". This summer of microfossil curation is actually her second position at AMNH. She's glad to be back. Future plans may include a stint in the National Parks, a fellowship in Indonesia, or anything else that comes her way.

The interns are supervised by the wonderful Bushra Hussaini, whose knowledge of the collections makes this enormous project much more manageable. We also are grateful to Lindsay Jurgielewicz for her help in coordinating the internship, Linda Scalbom for direction in the collections management process, and Ellen Thomas for her microfossil expertise.

After going through the inevitable paperwork that comes with a new job, Bushra gave us a tour of the invertebrate paleontology collections, which include the subset of ostracods and forams that we are working with. We were then each given our own projects. These were overwhelming at first, but we soon settled into a rhythm of writing out new labels, cleaning off dusty old slides, databasing, photographing, and cataloging specimens.

The picture below shows the sorry state some of these slides were in after almost a century of storage. The cardboard of the slide decays and falls into the well with the specimen, and must be cleaned out very carefully with a small paintbrush. The ostracod pictured below is about half a millimeter in length.

Also in our first week, we went on tours of the vertebrate paleontology and anthropology collections. We were able to see some of what goes on behind the scenes at the museum. Preserving collections as extensive as those of AMNH is no small feat; we were able to see the care and thought that goes into collections management (not to mention the shelves full of triceratops skulls, a dinosaur brooding a nest of eggs, an incredibly well-preserved 2,000-year-old Andean carpet, and countless shelves full of incredible anthropological artifacts).

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