I am trying to reconstruct 8 hippocampal neurons in a 1 GB 3D tif image stacks with Vaa3D 3.20 to get neuronal trees (.swc).
my Vaa3D installation seems to have problems working with big image data. After cropping my brain hemisphere to a single neuron (48 MB) and additionally converting it with tetraconverter and saving as raw Vaa3D files, I could manage to do some computations.

Which neuron tracing plugins would you recommend?
Neuron2 APP1:
I need to decrease visual threshold to get good trees, pruning tree leafs (simple and multiple cover) seems to take most computation. That might explain, why formerly the program did not respond with the non-converted big image stack, even after waiting 4 h. If it works, it only creates a type of soma, no branches.
EnsembleNeuronTracerV2s:
Takes most time at "532test start". Creates a neuron more or less realistic but with too many branches. I didn't see any menu to set any configuration of the plugin. How to deal with it?
Beside that, it seems I have several bugs in the 3D viewer probably related to the complexity of the original image files as Translation not working.
Also I cannot drag/drop files into the gui as recommended by tutorials. It tells me that the selected file does not exist
I cannot access manuals, which are on your pages

You can try neuron2-APP2 first. "length_thresh" is the option to control the length of segments/branches.

Or you can try our new plugin UltraTracer to trace large-scale images.
Here is the paper; http://www.nature.com/nmeth/journal/v14/...
Here is the released Vaa3D with UltraTracer plugin: http://www.nature.com/nmeth/journal/v14/n4/extref/nmeth.4233-S2.zip

So what is your operating system (Mac, Windows, or Linux)? Which version?

Thanks,

Zhi

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APP2 works better, still not perfect, I will probably need to twitch the
parameters more. It does not capture the small neurites, which expose less
intensity and are thinner. Can you recommend which parameters to change?
Can I find a description of the different parameters?
I am currently working on Windows 7 Professional. We are considering to
install a Linux version. Would that make sense?
I downloaded the UltraTracer Plugin. Now I am a bit unknowledgeable in the
field; How do I integrate the plugin into the Vaa3D program? I copied the
resulting nmeth.4233-S2 folder to the Vaa3D folder and the program
recognizes the new folders and shows them in the menu, but it cannot access
the plugins themselves.

thanks,

If you can use APP2 without memory issue, you don't have to use Ultratracer, which is to boost base tracers including APP2 for large-scale image tracing.

There are three parameters you can try to adjust:
1. auto-downsample: uncheck to use full resolution image for tracing.
2. background_threshold: lower the threshold if the signal is too week.
3. length_thresh: i mentioned it before.

Zhi

Hi! I had a question, I'm really interested in using the Ultra Tracer. I downloaded Vaa3d for windows but it didn't come with the UltraTracer plugin. Where can i get this plugin for windows? I cant use the one provided in the link in the paper. 

Thank you!

Hej Zhi,

For huge images, APP2 still has problems. Would working on Linux facilitate Vaa3D computing?
I downloaded the UltraTracer Plugin. Now I am a bit unknowledgeable in the field; How do I integrate the plugin into the Vaa3D program? I copied the resulting nmeth.4233-S2 folder to the Vaa3D folder and the program recognizes the new folders and shows them in the menu, but it cannot access the plugins themselves. Is it because I am using Windows?