PiAutoStage

A system to digitize microscope slides

What is PiAutoStage?

PiAutoStage is a fully integrated system that is built around a new 3D printable design for a universally adaptable microscope stage. We have automated movement of the stage using low-cost small form computing (Raspberry Pi) and open-source microcontrollers (Arduino). By combining these techniques, we have created a device that can automatically capture the entire area of a microscope slide in a series of overlapping images that replicate the field of view and resolution of a traditional microscope.

The fully assembled PiAutoStage device made from red plastic. Blue servo motors are in the housings in the device.

PiAutoStage is a peer-reviewed article.

Before proceeding - please first visit the Open Access (free) peer-reviewed article on PiAutoStage. Much more detail is presented in this article and we promise that you will need it to make things work.

If you use PiAutoStage please cite:

Steiner, R. A., & Rooney, T. O. (2021). PiAutoStage: An Open‐Source 3D Printed Tool for the Automatic Collection of High‐Resolution Microscope Imagery. Geochemistry, Geophysics, Geosystems, 22, e2021GC009693. https://doi.org/10.1029/2021GC009693

PiAutoStage Creators

Headshot of R. Alex Steiner.

R. Alex Steiner

Ph.D. Candidate - Dept. of Earth and Environmental Sciences

Michigan State University

Headshot of Tyrone O. Rooney.

Tyrone O. Rooney

Associate Professor - Dept. of Earth and Environmental Sciences

Michigan State University

Building and using PiAutoStage

Designs for the basic 3D printable stage are hosted on Github as stl files.

Logo. A stylized microscope and microscope stage outlined in white is set into a black circle.

Stage Adaptability

Each microscope is different and may require editing of the 3D file to match screw patterns. We encourage contributors to the project to upload these modified designs to the Github repository and link to existing microscope models.


Logo. Python and Arduino logos are split in half diagonally and combined into a single logo.

The Python code and Arduino sketch software necessary to operate the motors and to capture images is stored on Github.


Digital rendering of the PiAutoStage where components are floating above on another in the assembly sequnce.

A list of recommended parts and basic assembly instructions is presented.


The PiAutoStage device mounted to a microscope stage. A thin section slide sits in the carriage. Wires connect to computer that is out of frame.

How do you use PiAutoStage to collect a series of compatible images?


Mosaic of red, blue, yellow, and green polygons with white space between the polygons.

How can you use widely available software suites to create a panoramic image of your microscope slide?


Photomicrograph of pink, orange, blue, yellow, green, and black minerals. Minerals have dark cracks in them.

Suggestions on how to efficiently deliver content to students


Black letters on white background reading "FAQ"

This is a free product - no one around here gets paid for development. So, problems will happen. We try and address them here but need your help too!


Leinster Granite rock sample in cross polarized light at 45 degrees rotation. Grey, black, pink, blue, and yellow minerals on a black background. image is 24520 by 14052 pixels and scale bar is 5000 micrometers long.

Leinster Granite, Ireland.

A collection of examples of how PiAutoStage has been used.

Questions?

FAQ Section

Contact us to get more information on the project