NITRC Vaa3D and Vaa3D-Neuron Forum: help

Vaa3D's raw file

Paul Bourke — Sat, 19 Apr 2025 23:57:47 GMT

Still looking .... where do I find the specification for the Vaa3D's raw file, I wish to generate them externally.

RE: Terafly look up table for visualization

Snehashis Roy — Tue, 15 Oct 2024 17:13:34 GMT

I am working with 16bit tif files. Does Terafly work with 16bit tifs? It is working with 8bit tifs, but not 16bit tifs. 16bit tifs after converting to Vaa3D format shows all zero.

Terafly look up table for visualization

Snehashis Roy — Tue, 15 Oct 2024 1:23:14 GMT

Hello,
I want to visualize Terabyte scale data (multiple 2D z-slices in a folder) in Terafly. I first converted them to Vaa3D multiresolution format using Teraconverter. Then I opened the RESxxx folder using Terafly. However, the 3d view is blank. I think what is happening is the image has large dynamic range but with very very high outliers (~65000) and 99th percentile is ~300. Is there a way to change the LUT of the view between a certain min and max?
Thank you.

RE: FlipY when loading stacked 2D .tif image

Hanchuan Peng — Wed, 07 Aug 2024 6:24:19 GMT

Originally posted by Jingyi Yao:
<blockquote>
Hello,
I'm trying to convert .tif image to .v3draw by command line vaa3d -x libconvert_file_format -f convert_format,
but the output image is fliped on Y-axis and i didn't find any parameter to prevent from this. Could you help me with it ? And how could I solve this problem ?
 
Thank you in advance!
 
</blockquote>
Yes the Y-flipping option can be set in the Preferences in the main menu!

FlipY when loading stacked 2D .tif image

Jingyi Yao — Wed, 07 Aug 2024 1:38:38 GMT

Hello,
I'm trying to convert .tif image to .v3draw by command line vaa3d -x libconvert_file_format -f convert_format,
but the output image is fliped on Y-axis and i didn't find any parameter to prevent from this. Could you help me with it ? And how could I solve this problem ?
 
Thank you in advance!

DIfferences in the number of stacks when saving the swc files as masks

suganya sivagurunathan — Wed, 01 May 2024 15:27:38 GMT

I used Vaa3D-APP2 to trace the neurites in an image and saved the swc file as mask using the swc_to_mask. Although I can specify the image size, the saved mask always differs from the original image in the number of Z stacks. I have tried unchecking the `Radius in 2D` while tracing the neurites. Even then I observe the changes in the number of stacks when saving the masks. Is there a way to fix this?

RE: Changing color on 3D traces not working

Lingli Zhang — Thu, 30 Nov 2023 7:32:56 GMT

Hello Muhib Methani,
there are several methods to help you to change type:
1, you can just drag the swc file into vaa3d, Ctrl-L to enter the line mode, and selete any curves,choose Alt-T, there will be a dailog to let you choose the color you want;
2, you can just write an python script, change the second column of swc files, the each row of swc files means (n type x y z r parent), change type you wanted.
If you have anyother problems, please tell me. 
Best wishes,
Lingli

RE: convert tiff to v3draw via plugin in newest Vaa3d version

Lingli Zhang — Thu, 30 Nov 2023 7:24:57 GMT

Hi Bea,
you can try convert_file_format plugin to covert v3draw to tiff or tiff to v3draw, or the bioformats plugin has been solved in the latest Vaa3D-x version, you can download it （<a href="https://github.com/Vaa3D/release/releases/tag/v1.1.4">Release Vaa3D-x Release 1.1.4 · Vaa3D/release (github.com)</a>）and if there is any other problems, we will be glad to slove it, thanks!
Best Wishes,
Lingli

swc_registration.exe crashes silently for larger reconstructions

bea collibee — Thu, 19 Oct 2023 12:01:11 GMT

Hello, I have a whole-brain neuron reconstruction which I would like to register to the CCF using the swc_registration function provided with mBrainAligner. The function outputs a global_data.swc, FFD_data.swc, and resample_data.swc. However, it terminates before outputting local_registered_data.swc when I run it on my own reconstruction. 
I have played around with resampling the reconstructions to different step sizes, in case it is an issue of the size of the reconstruction (the original reconstruction SWC is 1.5 MB, ~40k nodes). Without any resampling, the program crashes before starting the local registration step.
On the resampled data (100-300KB), the local registration step seems to run, but crashes at some point before finishing, so no local_registered_data.swc is saved. 
Attached is a snapshot of the output log before the program crashes. 
Can you help?
Many thanks!! 
Bea

Changing color on 3D traces not working

muhibmethani — Tue, 19 Sep 2023 13:38:15 GMT

Hello,
I am trying to change the color by SWC file type on Vaa3D. The way I work with my traces is I first edit them in neuTube and assign SWC file types to each branch according to the standard method: 1 is soma, 2 is axon, 3 is basal dendrite, etc. I can change the colors on neuTube but when I save them and open the traces in Vaa3D, it gives me a black soma with pink and red projections--something I would like to avoid. When I go to the object manager to try and change the color, it says that the entire neuron is a single trace and thus I can only change the color of the entire neuron, which is something I don't want to do. I want to see if I can make the soma yellow, dendrites blue, and axons red.
 
If you would like to see what I mean, attached are the traces for the neuron.
 
How would I go about doing this?
 
Best wishes,
Muhib Methani