Hello, I am the Geological Mapping Technician for the Geology Department at the University of Otago.
If you need any assistance with any topics that you consider could be related to technical aspects of geological mapping please come and see me or send me an email.
Topics include: geology software, general illustration software, GIS software, mapping hardware (UAV/drone, GPS, cameras) and more.
This article has been specifically written for using the macro-photography setup or the stereomicroscope setup in the Imaging Lab (formerly called the Graphics Lab) in the geology department. Instructions are for using Zerene stacker to stack the images rather than photoshop because it is faster, easier and produces better results in all cases that I have seen. For example Zerene Stacker took 72s to stack 11 images and photoshop took 125s, the difference in stacking speed is even more pronounced when more images are used.
This post supersedes the previous focus stacking post I wrote which recommended using photoshop.
This article has been specifically written for using the macro-photography setup in the Graphics Lab in the geology department and Adobe Photoshop CS5. Concepts are applicable to other equipment and versions of Photoshop.
I have made a new post with instructions using Zerene stacker to stack the images rather than photoshop because it is faster, easier and produces better results in all cases that I have seen. For example Zerene Stacker took 72s to stack 11 images and photoshop took 125s, the difference in stacking speed is even more pronounced when more images are used.
We want images stacked
Sometimes we capture images of the same area (e.g. a particular part of a thin section) using different conditions (reflected light, PPL, XPL, Cathodoluminescence) . We may then want to stack the images together so that we can see how each different mineral, for instance, appears under the different conditions.
We can align objects manually because we see recognisable features in each image. It can be a little tedious and difficult trying to add, manually align, resize and rotate the images in software like: Adobe Illustrator, photoshop, the gimp, image j or other software.
There is a semi-automated way to speed up this process in photoshop. I’m not sure of the exact conditions under which this will actually work. But it’s fairly easy to try and could save you a load of time.
How to do it
The first thing we need to do is to load all the images as layers in a photoshop document.
- Open photoshop
- Go to file>Scripts>Load files into Stack
- Navigate to the folder with your images in it and load these.
You should now see all your images as layers in photoshop with names corresponding to file names (handy eh?).
- Select all the layers by clicking on the top layer and then shift clicking on the bottom layer. They should all have a blue background in the layers panel indicating they are all selected.
- Now go to edit>auto-align layers
- I recommend trying collage first which will not distort the image.
Thanks to Steve Kidder for working this out with me.
A few people have been using the Cathodoluminescence microscopy (incl. image capture) equipment that Brent Pooley and I set up. We have, until now, been sharing the image capture part with the photomicrograph setup in the Graphics Lab. This was quite inconvenient and it meant that the Photomicrograph setup, which gets used a lot, was often unavailable.
We are pleased to announce that we now have a dedicated Cathodoluminescence microscopy (incl. image capture) setup. This also means that the Photomicrograph setup will now have uninterrupted availability. Instructions and training are available for both setups, contact me (photomicro, CL) or Brent (CL) for training.