I’m working on an independent experiment, and I’m attempting to separately segment the granules out of an SEM image of a material. The issue is that the granules are too close together and the lighting is non-uniform.
I’ve tried the Threshold tool, that doesn’t work well since the outlines of the granules are a wide swath of dark shades rather than just one shade, and the granules are too close together.
I’ve tried a tool called Weka Trainable Segmentation, which allowed me to trace the granules and outlines manually, and create a binary image that seemed to work, however not only was this method tedious with long wait times, but it also wasn’t precise enough as I repeated the measurements a handful of times, and the mean area distribution of the granules changed significantly each time after analysis.
The closest I got was adjusting the brightness of the image using “Curves” in photoshop, which raises the dark portions of the image up and flattens the lighting so all granules look like they’re in a uniform light, and THEN I used a combo of “Find Maxima” and “Threshold” on the darkest areas, and used Image Calculator with an operator of AND to combine both images. That gave the closest approximation of outlining the particles, but it still wasn’t 100% perfect.
So, as a plan B, I was recommended to seek help from an imageJ help website, and now I’m here. I would post a picture of the image I’d like to segment to show you guys what I’m trying to do, but I guess I can’t attach images because I’m a new user?