Simple Neurite Tracer --Tracing Preferences

I am experiencing issues while using the Simple Neurite Tracer plugin, and I hope that someone has the knowledge on how to fix this (i.e. changes in settings somewhere). I start a path by clicking on a dendrite, but when I click the second time to create a path, the program prefers to trace along on the way outer edge, as if it is avoiding tracing the dendrite. It’s as if the plug-in’s preferences are for darker shades of the image (the dark background) rather than the brighter shades (the white dendrites). What’s strange is this only happens on a few images, but this weird issue makes it very difficult to trace these few images accurately.

The version of ImageJ I am using is 1.52p.

Welcome to the forum @salem44!

That sounds strange indeed, are you using the latest version of SNT? (available through the Neuroanatomy update site)
It sounds like there could be an issue with the image, would you mind posting a snapshot of the image properties? They can be seen by going to Image > Properties

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Hi! Thank you for replying; I did your recommendation, but sadly the settings for both the normal and abnormal images were the same. I wasn’t using the latest version of SNT because the last update I saw appeared to have a fewer amount of available tracing tags which was crucial for my project, but the good news is that tonight I figured out how to fix it! On the SNT pop-up window, I clicked on “Pick Sigma Manually,” and then I lowered the sigma from its default value of 0.0977 to high and low numbers. It seems to change based on where I’m tracing on the image. I clicked on “Hessian-based analysis” (to check its box), and now it’s fixed! :slight_smile:

Hi @salem44, can you please detail this better? It has been quite the opposite. All of the tagging options have been significantly improved with recent versions.

Glad you got it working. Do have a look at the documentation where Hessian analysis is explained. For a more in-depth insight have a look at SNT’s preprint (Fig. S1), that describes the effects of the Hessian parameters in tracing performance.

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