Rectangular to hexagonally shaped orange, blue, and white crystals on a black background. Crystals have concentric growth zones of varying colors.
This image was captured in cross-polarized light of a crystal-rich lava from northern Kenya. The lava contains abundant, chemically zoned clinopyroxene crystals that record a history of magma interactions. Credit: Steiner and Rooney, 2021,

It all started with a problem many geoscientists faced in 2020.

Alex Steiner, a doctoral student at Michigan State University, had research to do working on thin sections—slivers of geological materials that are usually analyzed under a microscope. But he and the two undergraduate students on the project were not allowed to access the lab or the geological samples they were working on. Because, well, pandemic.

It was out of this necessity that Steiner helped develop a new tool that could automatically take pictures of entire thin sections and stitch them into digital panoramic microscope images that could be analyzed anywhere.

The technical report on the device, named PiAutoStage, was recently published in Geochemistry, Geophysics, Geosystems.

Because thin sections are also commonly used for instruction in geoscience lab courses, PiAutoStage could also provide instructors a new, affordable resource to digitize and use specimens and literary materials they already have curated in their curriculum.

“I think this is a really nice approach to a problem that I heard a lot of people talking about last year when everything moved online,” said Anita Marshall, a geologist at the University of Florida who was not involved in the study. “Anybody that had any sort of microscope work in their courses really struggled to move that work online.”

Getting Microscopy Online

PiAutoStage consists of an open-source mechanism that moves the sample around the microscope, attached to a high-resolution integrated camera and inexpensive Raspberry Pi computer. The researchers wrote computer code to take hundreds of high-resolution images of an entire microscope sample and combine them into a single panorama.

Three image mosaics of a fragment of Earth’s mantle collected in three optical arrangements with the PiAutoStage: (a) plane-polarized light, (b) cross-polarized light, and (c) cross-polarized light at 45° of rotation. Three sets of images permit students to examine minerals and rock textures in a way that replicates the experience of using a petrographic microscope. Click image for larger version. Credit: Steiner and Rooney, 2021,

This technique allowed two undergraduate students—one at Michigan State University in East Lansing and another at Wayne State University in Detroit—to work collaboratively on the same project at the same time using the same thin sections of a flood basalt sequence, said Tyrone Rooney, a geologist at Michigan State University and senior author of the paper.

And for the most part, the students enjoyed working with the microscope images online, Steiner said. “Because the interface behaves the same way as things like Google Earth or things like that. It’s just zoom in, zoom out, click and drag around. So they picked it up real quick. I don’t think anyone had any complaints, even with the very first lab we ran this year.”

One downside to long-distance microscopy, however, is its difficulty in replicating the collegiality that comes with the ability of “students to be able to shout across [the room] to another student, ‘Hey, what’s this?’” said Rooney. The researchers tried to replicate this interaction by allowing students to share panorama views with one another.

The software also does not replicate all the different functions of a microscope, Rooney said. “You don’t have the ability to use a lot of the advanced tools that are in a microscope that help students identify ambiguous crystals.”

Despite these limitations, “from the perspective of a broad teaching tool, we think it’s useful and in fact is different to a microscope,” Rooney added. “Previously, students would not have actually been able to see the entire area of a microscope slide in a panoramic image.”

More Accessible Geoscience

“In a postpandemic world, devices like this could still be used for teaching. It allows students to have access to samples, for example, that might be very valuable and can’t be left in the lab, or there aren’t enough thin sections for an entire group.”

“In a postpandemic world, devices like this could still be used for teaching,” Rooney said. PiAutoStage “allows students to have access to samples, for example, that might be very valuable and can’t be left in the lab, or there aren’t enough thin sections for an entire group.”

Although resources that can image microscope samples already exist, they can often be prohibitively expensive: Microscopes with built-in or add-on cameras can cost tens of thousands of dollars.

By contrast, because the PiAutoStage mechanism is entirely 3D printed, it would cost less than $200 to make the device, said Steiner, who was lead author of the paper. “You don’t have to order the parts from anybody or anything like that. You can literally make all of the hardware—it’s all printed and assembled, [and] basically, it snaps together.”

The system is also open source and made to be adaptable to almost any microscope. The researchers have also set up a PiAutoStage website detailing examples, instructions, and FAQs to help others build their own device.

The new technique could make future research into thin sections more accessible, Rooney said. “With more of these devices out there more innovations will happen simply because more people are trying to use it. I don’t know what will happen. All I can say is when we introduce a new tool, usually data follows.”

The images produced by PiAutoStage also have one additional benefit.

“Just looking at the thin section imagery that I’ve taught with for years in a different way, I’ve seen them in a different way,” Rooney said.

“All the petrologists that have seen what this is have also responded with, ‘This is so cool.’ In fact, that word seems to be one that is used quite an awful lot,” he added.

—Richard J. Sima (@richardsima), Science Writer


Sima, R. J. (2021), A new tool may make geological microscopy data more accessible, Eos, 102, Published on 27 May 2021.

Text © 2021. The authors. CC BY-NC-ND 3.0
Except where otherwise noted, images are subject to copyright. Any reuse without express permission from the copyright owner is prohibited.