SNT (Simple Neurite Tracer) and synapses

[Niko Ehrenfeuchter]

Dear all,

in his announcement [1] to this list about updates on the Simple Neurite
Tracer from April 2011, Mark Longair wrote a section about colouring the
paths according to values in another stack / channel, e.g. with a
synaptic marker.

I'm wondering if anyone has more details about how to do this, or even a
snipped of code, as we're having exactly this use case right now that
we'd like to solve using SNT...

Thanks a lot!
~Niko

[1]
http://imagej.1557.x6.nabble.com/update-on-Simple-Neurite-Tracer-td3684924.html
--
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University
of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: [phone] | [hidden email] |
www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

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[Tiago Ferreira-2]

Dear Niko,

It is a neat feature. There is not much more to add to the description you have,
apart that it requires the 3D viewer, as SNT overlays in the main tracing canvas
are not affected by it.

Here is a step-by-step:
1) Open the stack to be used as coloring mask.
   This can be an RGB image or a grayscale image displayed with your favorite LUT
   (It can also be a synthetic image, e.g., as the one displayed in the example
   at http://fiji.sc/Simple_Neurite_Tracer:_Sholl_analysis#Sholl_Image)

2) Open the tracing stack

3) Open SNT. Make sure you choose a 3D Viewer under "Choice of 3D Viewer"

4) Once you obtain the traces from image 2), select image 1) under the
   "Use colors/labels from" drop-down menu.
   Paths in the 3D viewer will be rendered according to the displayed colors of
   the chosen image, i.e., each voxel associated with the path will be painted using
   the color of the same voxel of the labeling image.

Because the "Choice of 3D Viewer" is only available with 3D stacks, this feature
does not work with 2D images. However, if you are tracing 2D images you can always:
1) Export your traces as swc (.traces file keep track of image depth)
2) Close SNT
3) Append an empty slice to your images (Image>Stacks>Add Slice)
4) Re-initiate SNT and load the exported swc traces

Best,
-tiago
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