Pond Scum

It's time for a hike! So I grab a handful of pipettes and a plastic cup to carry them in. Whenever we come across some particularly scummy water, we sample it with a pipette. I put the pipette into the cup upside down and put the cup in my pocket. When we get home, we look at what we caught through our microscope.

I get the pictures and movies simply by pointing my camera down the eyepiece of the microscope and snapping. Who knew it would be so easy!

The pictures titled "Helicon Focus" were done with this software. It takes a bunch of pictures with a shallow field of focus and combines them into one with a deeper field of focus! I want to play with it some more.

When my license for Helicon Focus expired, I determined to find another way to do this. I'm pretty happy with what I came up with. First, I make around a 5 second movie of the subject while slowly rotating the fine focus knob on the microscope. Then I use ffmpeg to convert the movie to a series of stills. (The combination of forward slashes and Windows executables is because I use the cygwin terminal to run these commands.)

ffmpeg/bin/ffmpeg.exe -i video.mp4 -r 10 -vf "scale=1920:1080" output_%4d.png

Then I align the stills using Hugin.

Hugin/bin/align_image_stack.exe -m -C --gpu -a OUT output_00*

Then I use EnfuseGUI to combine all the images. In the GUI I add all the TIFFs I got from the align steps and set the bracket count to the number of these images that I have. I set Exp. to 0, Cont. to 1, Sat. to 0 and check "Force hard blend masks."

Finally I use Photoshop to adjust the image levels.