A 300-DOLLAR KIT TURNS A DECADES-OLD LAB MICROSCOPE INTO AN AUTOMATED SCANNING SYSTEM
A three-hundred-dollar kit turns a decades-old lab microscope into an automated scanning system.
by D Ehrlich, Y Rosen, D F Parks and colleagues
ScienceOpen-hardware
Built withRaspberry Pi3D printing
- difficulty
- ●●●○○
- time
- a weekend
- license
- CC BY-SA 4.0
- repo
- repo FINISHED0 stars
●●●○○ · a weekend · CC BY-SA 4.0 · 0 stars · repo FINISHED
WHAT YOU’LL NEED
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COMPAREE VERDICT
This is automation for a microscope you already own, not a microscope kit. If your lab has a decades-old inverted instrument that lacks X-Y scanning and focus stacking, this retrofit replaces the fine-focus handwheel with a stepper on a flexible coupling, adds an X-Y stage built from two small NEMA 11 lead-screw rails, and pushes images to cloud storage for about three hundred dollars. The authors built it on a twenty-year-old Zeiss Axiovert 25 and show focus stacks of a honeybee and stitched scans of mouse stem cells and organoids — the kind of consistent datasets machine-learning microscopy work needs. The build uses Pololu Tic controllers, a mix of PLA-printed and laser-cut stainless steel brackets, and an optional foot pedal for hands-free capture. The hardware is CC BY-SA 4.0 with files on OSF. The single biggest trap is compatibility: the brackets were designed around one microscope, and the paper does not list other models that will take it. The second is precision: the authors call positioning repeatability the main drawback (the Y axis returned within a 165 µm range), which stitching software hides but precision work will not. If it fits your instrument, this is a weekend project that turns an old microscope into an automated imaging station.
IN THE REPO
GOOD TO KNOW
- —CC BY-SA 4.0 licence permits commercial use.
- —Files are published on OSF at doi 10.17605/OSF.IO/R8PDX, not in a GitHub repository.
- —CAD files for printed brackets, a full BOM with Pololu Tic stepper controllers, and the Python capture scripts (OpenCV, tkinter GUI) are all on OSF.
- —The paper includes assembly instructions, wiring diagrams and example imaging protocols.
- —Designed specifically for inverted microscopes with accessible stage and focus knobs; not every legacy model will fit.
- —The 300-dollar figure is for the retrofit kit only — you need the legacy microscope already.
Parts to buy
5 itemsFrom our check of the build. Exact quantities and part numbers are in the creator’s BOM.
Can I build this?
Build at your own risk. Projects involve tools, electronics and sometimes mains voltage — follow the creator’s safety notes.
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Start here
Navigation into the creator’s own docs — we don’t rewrite the guide, we route you to the source.
- 1.Download the files from OSF (The CAD files, BOM, wiring diagrams and control software are all on OSF at doi 10.17605/OSF.IO/R8PDX.)
- 2.Check compatibility with your microscope(The brackets are designed for inverted microscopes with accessible stage and focus knobs. If your instrument has recessed controls or unusual geometry, you will need to adapt the CAD files.)
- 3.Order the components from the BOM(A NEMA 17 focus motor, two NEMA 11 linear rails for X-Y, Pololu Tic drivers and an optional foot pedal. The paper lists specific part numbers.)
- 4.Print the PLA plate holder and stage brackets, and have the stainless steel and acrylic parts cut(Standard FDM printing; no support structure or exotic material required.)
- 5.Follow the assembly and wiring instructions in the paper (The paper walks through mechanical assembly, Pololu Tic settings and the Python capture scripts for focus stacks and X-Y scans.)
KNOWN ISSUES
- The 300-dollar figure is for the retrofit kit only — you need the legacy microscope already. If you are shopping for a complete imaging system, this is not it.
- Designed for inverted microscopes with exposed stage and focus knobs. If your instrument has recessed controls, an unusual geometry or integrated motorisation already, the brackets will not fit without modification.
- The paper does not list every compatible microscope model. You will need to measure your own instrument and check the CAD files before ordering parts.
- The setup was built and tested on Windows 11 with the Pololu Tic control software and an Elgato Stream Deck for the pedal; on another OS you will need to rework those parts of the control chain.
- The stepper motors are not encoded, so there is no absolute position feedback. If a motor skips steps during a scan, the system will not detect it.
- The paper demonstrates the system on specific cell types and organisms. If your imaging protocol has tighter requirements for vibration, speed or precision, this retrofit may not meet them.
Does this work on upright microscopes?
The published design is for inverted microscopes with accessible stage and focus knobs. An upright microscope would require redesigned brackets and possibly different motor placement.
What cameras does it support?
The authors used a Raspberry Pi HQ camera connected over USB through an Arducam CSI-to-USB adapter, and their Python code grabs frames with OpenCV — so any camera OpenCV can open over USB should work, though you may need to adjust resolution settings in the scripts.
How precise is the X-Y positioning?
The paper measured it: after ten 50 mm out-and-back moves per axis, the X axis returned within an 11 µm range and the Y axis within a 165 µm range, which the authors blame on friction at the far end of the cantilevered rail. The steppers have no encoders, so skipped steps are not detected; for stitched scans the stitching software absorbs the small errors, but precision-dependent work may need more.
Can I use this for live-cell imaging over days?
The paper does not demonstrate long time-lapse runs; it shows focus stacks and stitched X-Y scans. For multi-day live-cell protocols you would need to verify yourself that the motors and the double-sided-tape-mounted focus bracket stay put, that the stage is stable, and that any environmental chamber does not interfere.
What is the cloud storage setup?
The authors upload images to an S3 object store (Ceph on the National Research Platform), browse them through a Nextcloud dashboard and back up to Amazon Deep Glacier. Because it is plain S3, you can point it at most cloud providers — or keep everything on local storage.
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Discussion1
FROM THE COMPAREE TEAM
The paper names Thorlabs MLS203-1 and MFC1 as the commercial analogues but does not publish their prices — if you have priced either system, what does this retrofit actually save?
D Ehrlich, Y Rosen, D F Parks and colleagues
The team at the UC Santa Cruz Genomics Institute published this work in HardwareX to address a practical problem: computerised microscopes produce the large, consistent datasets that machine-learning microscopy needs, but most academic labs cannot afford them while owning legacy instruments with excellent optics. The retrofit automates those legacy systems for three hundred dollars.
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- Information is provided without warranty and may become outdated as projects evolve. Prices are indicative bands only — always check the creator’s parts list for current costs.
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CompareeTEAM28d agoedited
Practical notes from our verification: the files live on OSF rather than GitHub, which is fine but means no star count or commit history to check activity. The paper is detailed on assembly: a NEMA 17 stepper replaces the fine-focus knob through a flexible coupling, two NEMA 11 linear rails handle X-Y, Pololu Tic drivers run the motors, and a Raspberry Pi HQ camera connects to a Windows 11 PC through an Arducam CSI-to-USB adapter. The software is custom Python with OpenCV and a tkinter z-stack interface. The single biggest decision is compatibility: the parts were built for a Zeiss Axiovert 25 inverted microscope, and the paper says they may not fit every microscope but provides editable source files so you can adjust dimensions. Measure your instrument before ordering parts. There is no build video. Correction (4 October 2026): we re-checked this page line by line against the project's own repository, documentation and videos, and fixed errors in earlier versions.