SNT Image Analysis

For SNT tracings can you use Max Intensity Projections of Z-stacks? Has anyone tried this or have any helpful suggestions for a beginner? Help is greatly appreciated.

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Welcome to the forum @Jessica_Sidisky,

You can certainly use either! As per beginner suggestions: I would recommend you have a look at the introductory video tutorial by @arshadic as well as the detailed Step-by-step instructions.

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Hello,
Thank you for your reply and the recommendation. I really appreciate it. Since my post I have been working on the tracings between both the z stack and the MIP and found the zstack easier to work with with no real difference in the analysis between both methods. I have found the videos and instructions super helpful.
Thank you for your help.
Best,
Jessica

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Hello Again,
I am currently working on how to best optimize my tracings. I had a quick question in regards to the path fitting feature. I was wondering on thoughts or suggestions of this feature from anyone who may have experience with it. I looked through the SNT guide and walked through and was able to understand the specifics and instructions. I was more curious about this feature for optimizing traces before analysis.
Thank You,
Jessica

Hi @Jessica_Sidisky,

SNT provides several points of access to the path fitting functionality, some of which may be better suited depending on your analysis needs. Paths can be refined both via GUI commands and the scripting API:

1. Fit Paths via the Path Manager GUI

This mode is useful if you need to optimize the Paths of a single tracing or parts of a tracing. To refine a subset of Paths, select a group of Paths in the Path Manager prior to running the fit. To refine all of the Paths in the Tree, leave all Paths deselected.

2. Fit Paths via the scripting API

This route is helpful if you need to batch-optimize a set of tracings. There are some scripting examples in this thread demonstrating usage. Just like in the GUI, the fitting routine may be applied to any subset of Paths as you see fit (no pun intended).

Please let us know if you would like more information specific to your use case.

Hi,
Thank you for you suggestion. I appreciate the help.

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