First - I deal with Java plugins, and have very little experience with the GUI or macros. I’d like to keep it that way for this project. I’m trying to build a completely automatic segmentation program, in Java. The task is relatively simple.
I have a segmentation task involving size and shape - but also location in the image. I could live with sketching a polygon around an ROI, but would prefer to instead use distance from the center of the image (and include only regions which are close to the center of the image). Experimenting with the GUI, using global thresholding and “Analyze Particles”, I have gotten to the point where filtering on size and circularity is giving me good results - with a few stray regions outside the region I care about. So…I’m now ready to write Java code to look at the results of “Analyze Particles” and filter based on location. One option is to create a mask and then edit the mask, based on either a manually drawn polygon, or distance from the center of the image. That’s my current first choice - I can do that without any assistance. Another option is to loosen the criteria used by “Analyze Particles” and then do further filtering of a list of regions. This is where I need help. I have no experience with generating, and then processing, a list of regions produced by “Analyze Particles”. This looks like a good opportunity to repair my ignorance. What API’s should I look at? How do I invoke “Analyze Particles” from Java, and how do I access the results? Secondarily, I’m finding that “circularity” does not completely capture the shapes I’m interested in. I’d appreciate pointers in methods of analyzing individual segmented regions, specifically to eliminate long, thin regions. ROI filtering (or distance from the center of the image) will probably be sufficient - but I’d like to have both belt and suspenders. Finally, I may be interested in measuring various properties of the segmented regions, such as perimeter, etc. Ideally, I’d like to see example Java code that runs “Analyze Particles” and then processes a list of particles. Macro code would be fine - I can translate from that. Probably sufficient is a list of APIs to look at. All clues gratefully appreciated. If absolutely necessary, I can provide a few sample images, but I’m really not authorized to publish these images widely. -- Kenneth Sloan [email protected] Vision is the art of seeing what is invisible to others. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
