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fiji / SNT

Legacy project superseded by https://github.com/morphonets/SNT
GNU General Public License v3.0
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Neurite Tracer Algorithm for F-actin Skeleton Mask #58

Closed JEBrunsveld closed 4 years ago

JEBrunsveld commented 4 years ago

Hello Everyone,

I'm new here so let me introduce myself first. My name is Jesse and I'm a research technician at UMC Utrecht in the Netherlands. My goal is to learn some basic coding (Python and ImageJ macro) in relation to automated image analyses; I'm very new at this. My current challenge is an automated object/cell count on this image (and many more). Image1.

First I want to create a clean F-actin skeleton and use it for counting objects. I was experimenting with gaussian blur, tubeness and thresholding etc. with some quite good results. I discovered the simple neurite tracer and I'm convinced this will give me the best F-actin skeleton if I'm able to create a mask and have to click once... So this is my question: Is it possible for me to write a macro where it traces all F-actin lines and creates a mask without clicking? I know this is not neurite related but this will help me a lot with my macro. It would be much appreciated if someone can help me with this or point me in the right direction!

Thanks and best regards,

Jesse

ctrueden commented 4 years ago

@JEBrunsveld I encourage you to post your question at https://forum.image.sc in the "Image Analysis" category. The Image.sc Forum is primarily intended for questions like this, whereas GitHub Issues are intended for developers to track defects and enhancement requests for software components.

JEBrunsveld commented 4 years ago

I see. Thanks for the reply! I'll post my question over there.