Friday, 23 January 2015

Setting up focus stacking

I am trying to convert a flatbed scanner as a moving support for my camera for focus stacking. I'm going to document how it goes in case it helps others.

The idea of focus stacking is as follows:

  • I would like to take very close-up photographs of a gametophyte fern. 
  • I have a 5x Canon macro lens, but at the 5x magnification it only has 0.1mm depth of field.
  • In focus stacking the subject is photographed many times, and moved toward the camera a little each time. The many photographs are then combined into one single sharp photograph using commercial software (I'm using Helicon Focus).
  • With such a small subject it will be easier to make the moves using an electronic platform. 
  • I am going to convert a flatbed scanner so that I can put the fern on the arm and move the arm in tiny steps using a computer programme. 
  • The computer programme will run on a Raspberry Pi computer, which will also trigger the camera to take shots between moves. 

None of this was my idea. I learned it from the following sources:

It was recommended to me by Jim Haseloff of the Department of Plant Sciences in Cambridge. 

My hope is to set up a system like this and use it to support my own interest in photographing gametophyte ferns. 

I am hoping to take photos like this one of my own, but much better:

So how am I actually going to get this done? 

I'm using a Plustek OpticPro U12 scanner as it is quite an old model so is very solidly built, with a big strong platform on the scanner arm. This is it with the cover and glass platform taken off:

The motor inside is a unipolar one (shown by the fact that it has 5 wires).

The arm motor controls some cogs which push the platform along a metal pole.

There are two boards in the scanner as shown below:

The motherboard has a ULN2003 chip on it which we could use to control the motor, but I am going to buy a different one that will be easier to program.

I am going to hitch the scanner up to a Raspberry Pi by the method descriped in O'Reilly's "Raspberry Pi Cookbook".  To do that I have ordered:

- some male to female jumper wire
- an electronics breadboard,
- a chip called ULN2803
- a copy of the book.

We already have a Raspberry Pi and the means to connect it to my laptop via the network in our house.

I am going to work out how to set up the scanner arm to move forward in the correctly tiny steps at the correct speed, and then install software on the pi to trigger the camera to take shots in between steps.

This is just the first chapter of quite a long project. Hopefully more progress next week. :-)

The next page of this story is on this blog page.

This project eventually took wings and now has a website of its own. To see more about it please go to

Monday, 5 January 2015

The complex romantic life of the fern.

A gametophyte generation plant of the species Dicksonia antarctica.

The plant above is a gametophyte fern, which is, beyond doubt, the finest thing that ever existed in nature.

It is only about half a centimetre across, and it will never get very much bigger than this. What is it though, and how does it relate to the big ferns (like the one below) that we are more familiar with from our gardens?

A sporophyte generation plant of the species Dryopteris wallichiana.

Ferns are not quite like people in their mode of their reproduction. They have a system called "alternation of generation". In this system, a tiny gametophyte plant (top photo above) reproduces to make a new large sporophyte plant (second photo above). Then the large sporophyte plant reproduces to make a new tiny gametophyte plant. And round they go again, alternating between sporophyte and gametophyte for ever.

The two plants are both individuals in their own right, and they can live entirely independently of one another.

What are these sporophytes and gametophytes though?

A sporophyte fern is a large plant that produces spores. We can easily see the spores clustered on the underside of the leaves of ferns that we meet in the garden. The spores each have only one set of chromosomes. When they fall off the leaves of the large sporophyte fern, they land on the ground and develop into tiny gametophyte plants.

The tiny gametophyte plants have only one set of chromosomes in each of their cells. The plants never grow much larger than a centimetre across and at maturity (a few weeks) they produce egg and sperm cells which also only have one set of chromosomes. The sperm cell swims across the plant's surface and possibly even onto an adjacent plant, until it finds an egg cell and fertilises it. This fertilisation event produces a cell with two sets of chromosomes, which then goes on to develop into a large sporophyte fern plant.

It always astonishes me that something as deceptively simple as a fern has such a complicated life cycle. It actually includes two completely different kinds of plants, which take turns in living their lives.

Since some sporophyte ferns are large trees, this alternation of generation is the size equivalent of a skyscraper giving birth to a shoe, which then gives birth to a new skyscraper. It's pretty odd, and pretty amazing. What's more, the process has been going on quietly and successfully for many many more years than human reproduction, in spite of its complexity.

If you would like to know more about the gametophyte fern, or even grow some yourself, then you can find the instructions in my post called Growing Fern Gametophytes.