Wednesday, October 16, 2013

Setup for focus stacking

This is the second of a series of posts about using focus stacking to photograph insect specimens to illustrate identification works. The first part is here and provides a general overview. In this post I want to describe the setup I use to acquire the stack of images:

Setup for taking focus stacks ofa specimen
The photo shows my Canon EOS 60D with the MP-E 65 macro lens mounted on a Stackshot motorised focussing rail. This is mounted on a homemade jig which allows me to position the specimen vertically on the back wall of the jig and slide it sideways and up and down to center it in the field of view. The specimen is lit using three Yongnuo YN1410 LED video lights which give a bright, daylight balanced white light (I will write a separate post about lighting).


The jig

The jig. The insets show the vertical slider without the specimen carrier in place (bottom left) and the way in which the three flash brackets, used  for mounting the lights, are attached (top right).

My home made jig is built mainly from MDF. The base consists of a 32x14cm piece of 18mm MDF and the back wall is 25cm high, also 18mm MDF. They are joined by a couple of right angled steel brackets. The vertical and horizontal sliders on the back wall and the tracks they run in are all built from 3mm MDF. Three "Kood straight flash brackets" (bought off eBay) are attached to the back wall. These are used to mount the lights. The flash shoe has been removed from each of these brackets and an 8mm diameter hole drilled through the bracket where the shoe was located. These fit over three captive bolts glued into a piece of 2x1 which is then screwed to the top of the back wall. The brackets are fixed to the bolts using a butterfly nut so that they can be angled as required and held in place simply by tightening the nut.
Underside of base
The base has a 6x14cm slot cut in it and a 3mm Aluminum plate (14x20cm) attached over the slot. The plate has a series of 6mm holes drilled along its centre line. The focussing rail is mounted using a standard 3/8 inch photographic screw (also purchased off eBay). The black strip down the middle is a piece of cycle inner tube glued on with contact adhesive and helps prevent the focus rail from rotating out of alignment too easily.

Specimen carrier

Specimen carrierMounting pin
The specimen carrier consists of a 20x8cm piece of 3mm MDF which acts as the horizontal slider on the back wall. A 7x12 sheet of 12mm plastazote is stuck to it using double sided carpet tape (I usually get plastazote sheets from Anglian Lepidopterists Supplies). The background consists of a piece of paper pinned to the plastazote. A mid-grey background was used for specimen photos in Britain's Hoverflies, but a plain white background is shown here. I often see backgrounds with a coloured gradient on photos online - this could easily be achieved by printing the desired gradient using an ink jet printer and then cutting out a suitable sized piece to pin to the specimen carrier.

The actual specimen is mounted on a plastazote stage on a long pin to get it well in front of the background so that stays completely out of focus. The plastazote stage into which the specimen's micro pin is mounted has been coloured blue using a standard highlighter pen. This makes the mount easy to mask out of the finished image because this florescent blue is not a colour that is likely to occur naturally! (I will talk about post processing the stacked images in a later post.)

The second sheet of 6mm plastazote pinned to the bottom of the specimen carrier simply acts as a reflector. It throws some light upwards and tends to fill in any shadows underneath the specimen arising from the fact that there is no light below the specimen in my setup (although there is no real reason why you could not mount a fourth light on the base of the jig, below the specimen, if required, to get really flat, all round illumination).


Stackshot focussing rail
Stackshot controller
The StackShot "focus stacking macro rail" is a wonderful piece of kit, but is not cheap! As far as I know, it is only available directly from Cognisys in the USA ($525 + carriage at the time of writing). Remember that you will also have to pay import duty and VAT to HM Revenue & Customs when you import it!

The focussing rail is driven by a stepping motor which is controlled by the programmable controller. There are many options, but I use the one where you set the start and end point (by driving the rail forward and backwards using the "Fwd" and "Back" buttons on the controller) and step size. I set the step size using a Depth of Field table for the MP-E 65mm macro lens. I choose a step size that is 30% less than the Depth of Field for the F-stop and reproduction ratio I have set on the lens. This gives some overlap of the parts that are in focus between shots which helps the stacking software to merge the shots successfully. So, if the chart says that the Depth of Field is 0.5mm for my chosen lens settings, I would set a step size of 0.35mm (0.7 * 0.5). The controller works out how many steps of that size are needed to travel from the selected start to end points. When you tell it to start shooting the stack, the controller moves the rail to the preset start position, fires the shutter, moves by one step of the selected size, fires the shutter, etc. until it arives at the preset end position.

There are many options to control how fast the rail moves and the length of time between operations. For example, you can set how long to pause between the rail arriving at the next position for a photo and the shutter being triggered (i.e. how long to allow for vibrations caused by the rail's movement to damp down). It can be very useful to modify these settings, for example, to make the time between shots longer to allow a flash to recharge (if you are using flash to expose the shots). It also has an option to trigger the shutter twice for each shot so that you can use mirror lock up (as I normally do).

In the next post I will consider the lighting and compare flash and continuous LED lights.