I have found a way to build new plugins for ImageJ; I don't know how well this will work with using other Java features at the same time though.
Using a little bit in ImageJ I found that doing certain processes in order does have a positive effect on possibly grabbing at some of the diatoms.
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| Original Image |
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| Image with background removed (Process in ImageJ). |
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| Image with background removed, converted to binary. |
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| Image with find edges process, converted to binary, with holes filled in. |
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| Image with background removed, converted to binary, and holes filled in. |
The images still select a lot of garbage, but they select the diatoms as well.
By performing a Gaussian blur and then reconverting to binary you get much more defined blobs.
I wonder if doing a bit of blob analysis would isolate the good from the bad: circularity and area for example. In this image, the only useful diatom is the round one on the bottom?
ReplyDeleteFor test images, are you using one that you can verify and test with user segmented diatoms? In other words, are you using images that have diatom in the big HTML table page that we looked at on the first day? Make sure you're doing that so you have someway to judge your performance.