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! 

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 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.