Fluorescent Cell Calculator and Counter

Purpose

Here's what this app does: count cell bodies for you! Built specifically around the SSSIP program at Stanford, it is able to identify with 90% accuracy cell bodies stained fluorescently

This outshines any traditional method of purely manual counting, such as with ImageJ, automating the process*

*It's not fully automated, but performs well

How does this work?

1. The script first performs a simple filter over your image, boosting contrast and hiding or showing the RGB channels
2. Next, the script performs a brightness boosting algorithm by looking within a neighborhood double the size of a typical cell that you specify
3. Third, the script performs a thresholding pass to prepare the image for the final step
4. Finally, the script does a flood-fill pass over the entire image, scrubbing out all the cell bodies

Why was this made?

Well, when I participated in SSSIP in 2023, we were provided the same task: count transfection efficiency of a immunofluorescently-dyed image. All other three lab groups manually counted. I was lab lead, and being lazy, wrote a python program that performed just steps 3 and 4 of the process above. It was accurate enough for the time, but I wanted to develop the algorithm further. And here we are!

Anything else?

Interested in what I've done? Check out my website for more cool projects I've done!