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zitmen / thunderstorm

ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging
http://zitmen.github.io/thunderstorm/
GNU General Public License v3.0
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Background removal in ThunderSTORM? #66

Open bpisaacoff opened 6 years ago

bpisaacoff commented 6 years ago

Hi, is there any background subtraction or background removal tools in ThunderSTORM? I can't seem to find them.

Thanks,

zitmen commented 6 years ago

Hi, the wavelet filter does this for STORM images. If you are looking for more generic background removal, you have to look into IJ itself or other plugins.

bpisaacoff commented 6 years ago

Hi Martin, thanks for the quick reply.

If I am understanding Wavelet filtering (including it's application in ThunderSTORM) correctly what this is doing is extracting features of a given size and suppressing features which aren't that same size. Effectively this highlights the molecules in the image and suppressing pixel noise and any large scale features in the image. In the language of backgrounds, this could be interpreted as suppressing some background features. It is certainly not removing or subtracting backgrounds.

Do you agree with this interpretation?

Thanks,