Focus Stacking Fern Gametophytes Using A Flatbed Scanner

Background to the project

This is a focus stacked photograph of a fern gametophyte. The subject is about 3mm tall. My project at the moment is totry to take a series of photos of fern gametophytes as they develop from a single cell, until the point when the firstsporophyte leaf emerges.

The photograph above was taken using a Canon DSLR with an MP-E 5x macro lens and 4cms of extension tubes, to increasethe magnification to about 10x.

With this setup, the depth of field of the image is tiny, so that only part of the fern is in focus as below. In orderto have the entire subject in focus, I used a technique called focus stacking.

Focus stacking is a technique in which the subject is moved progressively toward the camera lens, with one photographbeing taken after each movement.

In the case of this photograph, the movement was carried out by mounting the subject on the arm of a flatbed scanner with the arm providing the movement. The scanner arm was edged forward in minute steps under the control of a RaspberryPi computer. The setup is shown below.

This close-up image below shows a larger specimen mounted on the arm of the scanner, as it works its way towards the Canon lens.

To create the fern photograph I took 40 photographs or slices. The photographs were amalgamated using software called Helicon Focus.

I have shown the photograph to some very experienced macro photographers in a forum online and they tell me that to get the image really sharp I should move up to using microscope objectives mounted on my camera, and ideally that I should build a rack and pinion mounting system with a stepper motor to control the movements of the camera relative to the subject. I've also to use cross-polarisation and more diffuse lighting.

This system would cost about £4000 to build and so I am trying to apply for a grant to design and build such a system.

My hope would be to design and build something related to this Bratcam setup, but very much more cheaply, using scavenged parts:

Here's my current best image again as a reminder of what I am aiming to improve upon.

To see the continuation of this project, please go to my next project.

This work was published in the The Pteridologist Magazine, 2017.