I am trying to remove small(yet brightly fluorescent) specks from a 3d image. These specks are very hard to get rid of using conventional filtering and are interfering with my subsequent image analysis.I was wondering if there is a plugin for ImageJ which allows you to selectively remove 3d objects.
I don't know of specific plugin that edits the base image based on particle size which is what you are describing. You can build a selective mask to filter your image using an combination of erosion and dilation operations. Then multiply the mask by your image to filter out your particles. Most of the operations in ImageJ are 2D as it is basically a 2D image processing program. Performing these operations are easily scriptable. With a little study, you can put together a macro that can do the filtration operation you want.
I hope his helps.
You can try FFT or Band Pass filtering. It´s frecuency domain-based filter that already appears on the Fiji menu:
Process>FFT>Bandpass Filer... and just indicate the size of the objects you want to filter.
Thanks to both of you! I have managed to filter out the small particles using filters included in the 3D ImageJ suite(http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start). It is not perfect since it converts your image to binary so I will look into your methods and see if these work beter.
Best,
Pieter
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