Is there any plugin or a way to filter ROI by a multitude of criteria? I have a macro to find cell ROI and vacuole ROI, but some of them have very inaccurate ROI and some are accurate. I know that cell profiler analyst may be able to use a training set to teach it to choose good fitting ROI, but I don’t know how that works or if you can import Fiji ROI. Mostly, I just need a way to discard sloppy ROI.
Here’s an example:
cell-1.tif (8.5 MB)
So… you could pre-filter which ROIs are created by setting different filters with Analyze Particles - namely the size and circularity filters. There also exists an Extended Particle Analyzer tool that expands the list of filters one can apply - this is available through the BioVoxxel Toolbox. To access this tool - you just have to enable it’s update site. Perhaps this is a good place to start?
sounds good I’ll take a look, any idea about removing ROI after they’re drawn?
Well… I’m not sure. Perhaps others have better insight in this… You could measure the ROIs - choosing whichever measures are most relevant in your case (looking at the list in Set Measurements). Then scan the Results table and delete those ‘bad’ ROIs… ?? Though I’m sure there are more refined ways…
Another tool for pre-selection would be the Shape Filter tool.