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A test case of a problem with image analysis of a vitrified latex specimen with Fiji/ImageJ
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README.md

README.md

Image analysis of a vitrified latex using Fiji/ImageJ

The specimen

The specimen was a soft polymer latex embedded in vitreous ice and imaged by cryo-TEM. The objective is to subtract the background (the ice has thickness fluctuations) and then segment each latex particle. We will use shape classifiers (circularity and aspect ratio) to select the isolated particles.

The scripts

The scripts are written in jython

Current issues

I'm trying a watershed based on this over-segmentation example.

The watershed segmentation has a problem. I need to figure it out...

Left: background subtracted, Middle: Gaussian Blur, Right: Classic Watershed Segmentation

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