Teaching Advanced Petrographic Imaging to Undergraduate Students

Petrographic analysis is one of the most fundamental tools in a geoscientist's tool kit. In much of the 20th century, scientists would provide detailed illustrations of what they were seeing through the microscope. Now, in the 21st century we have next level microscopic imaging that allows us to more effectively communicate this information. Particularly as of the 2020's we have advanced software that can stitch together petrographic images allowing for complete thin section photos. Why is this important? Because these photos are massive files with high resolution, meaning you can easily zoom into any part and get an HD visual, ultimately allowing for a more comprehensive and concise presentation. This method has been leveraged in research for a few years, but now that more user friendly software has been made available I think there is a case to be made for teaching this technique to undergraduate students. In the UTD Micro Imaging lab, I've done just that. Below I outline a step by step guide for how any university geoscience department with a trinocular petrographic microscope can teach their students how to create whole sample images.

Step 1: Download petrographic imaging software

This is sort of a prerequisite as I'm sure most labs already have software. However, I thought it was important to include this because out of the 10 or so imaging softwares I have personally encountered there are two that seem to be the most user friendly.

• Evident Scientific Cell Sens

• Leica Las X

Step 2: Choose a thin section

Any thin section will work, although samples with larger grains will take less time to stitch since they have less detail.

Step 3: Stage alignment

Align the stage so that the X and Y starting position are on an exact measurement. This will ensure that each photo is the exact same distance from the previous photo.

Step 4: Imaging

Now comes the tedious part. You will have to move the stage between each photo going all the way down the X axis in order to capture a single row of images. Once you reach the end of the thin section you will move up the Y axis until there is minimal overlap with the previous row. Then begin imaging the next row along the X axis going the opposite direction of the first row. Be sure that you are labeling the photo so that you can keep track of them in your files. This will become very important if you need to do any manual adjustments during stitching.

Step 5: Stitching the easy way

Once you have imaged the entire thin section head over to Autopano and start a new project. Then upload all of the photos when prompted and let the software take it away. When it has finished look over the photo to make sure there are no mismatches or overlap in the stitching. If there are, you will need to use a photo editor such as Adobe Photoshop or a free equivalent (I recommend Photopea as it is the closest to the real thing). Upload the stitched photo into the photo editor and use the cutting tool to cut away any mismatches or overlaps. As long as they are minor errors then you should be able to overlay the corresponding photo from your source file. You'll then want to adjust the opacity to about 50% and use the overlap to align it properly with the surrounding photos. Once you have don this you can crop it to fit the are that you cut and return the opacity to 100%. Don't forget to add the scale bar!

Step 6: Stitching the hard way

If Autopano isn't working or there are simply too many mismatches then you will have to sittich it manually in Photoshop or Photopea. Now, I know this sounds like a crazy amount of work but once you get in the groove it goes surprisingly quick. As long as you are only doing one or two thin sections this isn't too bad. Start a new project in your photo editor and set the canvas size to your desired resolution (bigger is typically better, you can always trim it after the fact). Drag and drop the photos individually starting with one of the corners. Everytime you drop in a new photo immediately adjust the opacity to ~50% and use the overlap to align it with the previous photo. You'll repeat this for as many photos as you have. Once you're finished you'll likely notice jagged edges and this is totally normal. Just go in with your crop tool and crop the edges off a bit.

Step 7: Admire your work perform your petrographic analysis

Be sure to take advantage of the fact that this is a digital product so you can add arrows and notes for mineral identification.