Desktop macroscanner

In this session I will detail all the components required to build your own macroscanner for less than £1k, excluding the camera. I’ll touch on some other focus-stacked 3d capture systems before focussing on a manual approach with this guide. This will keep costs down and ensure that output quality is maximised. This guide is best suited to patient people who have some experience with photogrammetry because it takes about a day to scan an object with this system.

My first look into scanning tiny things started back in 2020 during the Covid pandemic when I began searching for existing systems that used focus-stacking for photogrammetric 3d reconstruction.

The earliest example I found was developed by CSIRO Entomologist, Bryan Lessard and CSIRO Research Engineer, Matt Adcock for the Australian National Insect Collection in 2017. The system used focus-stacking but also an expensive computer controlled gimbal for a hands free scan. The aim was to scan quickly rather than achieve ultimate fidelity.

Another automated system published more recently in April, 2021 by Fabian Plum and David Labonte is an open-source project called scAnt that also uses a computer-controlled gimbal for positioning the specimen. The focus, like with the CSIRO system, is automation.

scAnt automated scanner (open source)

There are also micro structured light scanners available like the Artech micro, but these are not very high fidelity, don’t produce textures and cost almost £30k.

Given how novel focus-stacked photogrammetry is I didn’t want full automation yet. Focus stacking a hemisphere with an automated system would produce wasted photographs when viewing the flat side and sometimes an object may need more stacks taken in a certain area.

A manual approach is not only simpler to implement and less expensive, it’s capable of better quality and more efficient captures. I want to understand all the fine details and requirements for fidelity before looking at automation.

Focus-stacking is also extremely inefficient with only a tiny percentage of the photographed data appearing in the final images. Add to that the lossy nature of photogrammetry and it becomes clear we need as much fidelity as possible in the source data, so that is my focus with this rig.

Anatomy of the macroscanning rig

The macroscanner is made up of 4 primary elements; A camera and lens, a lighting system, a computerised rail, and a stage.

The camera and lens determine the quality of the final scan. The lighting system determines how much magnification is available for the scan. The computerised rail enables consistent focus-stack creation. The stage allows us to move and rotate the subject in a controlled and precise manner, without wobble.

Camera & Lenses

Sony A7R2

The camera is the primary barometer for scan fidelity so we want the highest resolution sensor possible.  Back in 2020 the Sony A7R2 was my choice with its full-frame mirrorless design. Its 42.4 mpx sensor produces images at 7974 × 5316 resolution which, in my view, was just enough to make acceptable scans. This camera has been superseded by the A7R4 with a 61mpx sensor, at the time of writing.

In order to capture objects between 1x and 5x magnification I use two lenses – The Laowa 100mm 1-2x macro. and the Laowa 25mm 3.5-5x macro.

Laowa 25mm macro 2.5x to 5x

Laowa 100mm macro 1x – 2x

lighting system – flash

KX800 flash system

Godox 64 work-light

The lighting system is very important for macro photography. As magnification increases so does the amount of light needed. Some macro rigs use ‘continuous’ lighting which means the subject is permanently lit rather than flashed. It is a method used in many automated systems but requires a lower shutter speed to work. Ultimate sharpness always suffers as a consequence. With a flash the shutter speed of the camera is locked at 1/200th which ensures perfect sharpness.

I settled for the KX800 flash from Venus optics which provides two flashlights on the end of flexible arms for under £300.  When cross-polarisation is required (for very shiny objects) I add linear polarising filters to the flashlight diffusers, and a circular polariser to the lens. It is important to only use cross-polarisation when necessary because it absorbs so much light from the system. Finally I use a single Godox 64 as a work-light for in-camera adjustments. This is mounted on a flexible snake, clipped to the desk.

Godox 64 on a snake

KX800 in position

Linear polarisation filters for the flash diffusers

Circular polarising filter for the lens

Focus-stacking rail & stand

WeMacro rail

Horizontal stand (showing WeMacro rail and large stage attached)

Focus-stacking rails have been around for years. There are a variety of products available, but they all do the same thing – they allow the camera to take a picture before advancing a tiny but precise distance before taking the next shot and so on. Some rails, such as the Mjkzz are capable of extremely small ‘steps’ down to fractions of a micron – 0.01 um in the case of the ultra rail, but this is overkill at the magnifications we are looking at. Given that our system is focussed on capturing objects down to 5x magnification, step sizes of a single micron are sufficient. I recommend the Wemacro rail for its low cost and computer-based interface. You will need both the rail and the stand in horizontal mode.

Wemacro rail

Horizontal stand

Stages – linear & rotation

Large linear stage

Small linear stage

Small rotation stage

Rotational stage and linear stage glued together

Stages are devices that allow for the very precise movement of an object. The movement of the object must not only be precise but also stable once a position has been chosen, with no ‘wobble’. Stages are either linear or rotational, and we need both to provide enough control of the subject to be scanned. The linear movement (x+y) is to ensure the subject is perfectly centred to the frame for each stack. The rotational movement is to provide precise angles for building the radius of stacks surrounding the object. The small linear and rotational stages are glued together with 2 part epoxy and mounted onto the large linear stage. This is then screwed to a plate mounted vertically to the stand.

Large linear stage

Small linear plus rotation

Connections & mods

Connectivity is straightforward with both a shutter release cable, and hdmi output going from the camera to the PC. The Rail controller is also connected to the PC via usb and is controlled with the Wemacro software; A simple gui that allows control of the rail at either mm or um resolutions. Modifications were made to provide mains power to the flash and the panel light instead of batteries.

The good thing about this setup is the convenience of using a pc for control; We have a nice big clear image of the camera output allowing for fine control of focus. Additionally, the size of the rig is very small without mini screens and controllers, allowing it to be placed on the desk next to the operator for easy access to the object for repositioning. Using this rig you can produce the stacks whilst working on something else!

WeMacro rail, stand, large linear stage and flash extension cable

Small stages, camera and flash extension cable connected

Complete system

Complete system

Flash and work light

Small and large stages

Flash extension cable connector

KX800 flash mounted to vertical plate

Next up – Using the macroscanning rig!