The Halfway Mark- Learning and Improving

The internship is halfway over and there have been quite a few exciting projects and finds in the first 10 weeks. One day, while conserving and cataloging specimens, a furry find was made. Inside a slide, right next to the specimen, was a larval skin of a beetle! How the larval skin got into the slide and how the beetle got out remains a mystery. This is a great example of why the conservation work we are doing with old collections is so important. 

There have been some really nice scans done of microfossils as well. Thanks to the Microscopy and Imaging Facility, we have started 3D printing some of the clearest CT scans here at the museum. It has, however, been a bit of learning curve.

Before you can even think about printing a 3D model, you must first spend time enhancing and editing the 3D image. Here at the American Museum of Natural History we use a program called VGStudio MAX. When a CT scan comes through you hope that the image is clear and that there is little to no sediment infill in the specimen. Even with a perfect scan, it still takes about 2 hours to have a printer-ready specimen. When the scan comes back with infill or "background noise" it can take anywhere from 4-8 hours to edit the image. At first every scan takes 5+ hours and the software can be tricky to get used to. Everyone is different, but I felt comfortable using VGStudio MAX by week 4.

Once you have edited your image, you are ready to start setting up your printing process. One factor we had to look at was which orientation we should print the specimens out for the clearest image. As seen below in the first attempt at printing out AMNH-FI 97614 Hopkinsina magnifica, the bottom model looks a lot nicer and smoother than the one on top.

Another problem is sizing. Because each specimen and scan is different, the scaling settings must be customized depending on the fossil. AMNH-FI 107593 Asterorotalia pulchella printed out too small and had to be redone so all of the details could be seen properly. 

Sometimes everything can be programmed correctly and the printing still go wrong. There were issues with the printer's plastic filament while printing out AMNH-FI 64208 Anomalina pacoraensis which led to this incomplete 3D model.

However, after a few mishaps and mistakes, we are starting to have a nice collection of 3D printed microfossils. 

From Top to Bottom: AMNH-FI 19954 Anomalina mantaensis, AMNH-FI 107593 Asterorotalia pulchella, AMNH-FI 97614 Hopkinsina magnifica

All smiles after printing out this unique foraminifera! 

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

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 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.

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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