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SNT: Manual

63 bytes added, 23 May
Tracing on Filtered Image
[[File:original-hessian-side-by-side.png|center|thumb|400px|OP_1 "Tubeness" image overlay at 80% opacity]]
===Tracing on Filtered Secondary Image===This is one of SNT's most advanced features. [[#Auto-tracing|Hessian-based analysis]] provides a convenient and easy way to perform auto-tracing on pre-process data in which voxels defining the traced structure are scored by their likelihood of ''belonging'' to a tube-like structure. However, it is just one approach for "tubeness" classification. What if your data requires different filtering?, or you want to experiment with other approaches?, or the perfect pre-processing algorithm for your images is not yet available in ImageJ? ''Tracing on Filtered Secondary Image'' is the answer to these questions: It allows you to feed SNT with pre-processed data on which the A*star search will operate. Here are two specific usages for this option:
*'''Frangi ''Vesselness'' filtering''' For certain datasets Frangi filtering ([https://link.springer.com/content/pdf/10.1007%252FBFb0056195.pdf Frangi et al. 1998]) is more effective than [[Tubeness]] at enhancing tube-like structures in the image. However, it is more computation intensive, and thus, less suitable to be adopted by the "compute-as-needed" approach used in Hessian-based analysis. Thus, one can import a pre-computed Frangi-filtered image using this option.
*'''Hessian-analysis at multiple scales''' Let's consider a structure formed simultaneously by very thick and very thin processes(e.g. axons and dendrites). To trace it one would need to adjust continuously the sigma parameter while tracing. Instead, to trace structures of variable diameters more effectively, one could load a copy of the Hessian current image associated with the second sigma could be loaded as ''Filtered Imagesecondary image'', and assign different hessian parameters to both images.
*'''Adopting probability maps''' Pre-classified images (using e.g., machine learning) could also be loaded here.
Importantly, this option can be toggled at will, during tracing. Indeed, one can ping-pong between ''filtered secondary image'' and tracing main image simply, by pressing {{key|I}}, the shortcut for the ''Trace on filtered Secondary '''I'''mage'' checkbox.
'''Filtered Secondary Image options''' can be specified in the ''gear'' drop-down menu, including commands for Loading/displaying the image file and the powerful ''Generate Secondary Filtered Image'' command:
[[Image:SNT-Tracing-On-Filtered-Image-Gear-Options.png|right|thumb|200px]]
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