Mineral Microscopy & Focus Stacking

I want to make it very clear that I am in no way an expert when it comes to using a microscope to view and photograph rocks and minerals but I think it would be interesting to have a page on the site here documenting the process of learning about this subject and I can share what I learn, as I learn it, here.

The microscope is a really important tool in the process of identifying rocks and minerals as it allows you to observe many features unseen to the naked eye. Also it’s just kind of mind blowing to look at.

My first exposer to the world of Microscopy in July 2021.

The microscope that I have is the AmScope SM-1TSZZ-144S-10M (Amazon Affiliate link) which has an overall magnification range of 3.5x-180x. Although this goes up to 180x I find myself mostly viewing specimens in the sub 90x range.

This microscope is a Trinocular scope which means it has a location to attach a camera which is extremely nice to have since the photos you can produce with the microscope are higher quality than what you can see with your eyes for most objects.

The process of taking photos using the camera on the microscope is really its own process and art form that requires some special software but the results can be amazing.

I’m using three different programs to accomplish these images. I use Amlite to control the camera, Zerene Stacker to focus stack the images and GIMP to do any post processing.

Focus stacking is a key element here since the depth of field on the microscope is a problem when viewing very 3D objects like rocks.

This is what that amethyst cluster looks like without focus stacking a bunch of images and just seen through the microscope.

Here you can see that only certain areas of it can be in focus at any one time.

I then use the Amlite software to take a series of photos as I adjust the focus depth from the top of the specimen to the bottom. Doing this will create anywhere from 15-35 good images that can then be focus stacked in Zerene Stacker.

Zerene Stacker looks at all of the images taken and uses an almost magical algorithm to figure out what is in focus and what isn’t. It then combines all of the in focus parts into one image. You can see on the left hand side is the output image and on the right there is some distortion which happens as you change the focus depth. This can be cropped out later.

This is what the final results look like!

Overall the results of the process can produce a high quality image that is fully in focus.

My next project is to get an adapter to be able to attach my Cannon 70D to the microscope which should yield high quality photos but the process for image stacking will still be the same.