NITRC Vaa3D and Vaa3D-Neuron Forum: open-discussion

Load the plug-in on the Mac version of Vaa3D

jazzbrain — Wed, 02 Mar 2022 7:26:24 GMT

Running Vaa3D on a Mac may sometimes not detect plug-ins. This is because of the Mac's defense mechanism. Simply use the sudo spctl --master-disable command and then allow developers from any source to load the plugin in general.

RE: Need help with neuron stitcher plugin

marinka88 — Tue, 20 Apr 2021 15:28:21 GMT

Thank you so much for your help!
I just updated the plugin, and the program works fine!

RE: Need help with neuron stitcher plugin

Yanyan Guo — Tue, 20 Apr 2021 8:50:51 GMT

Hi! I think the reason why the program crashed is that the Qt version is incompatible.

I downloaded the test data and the Vaa3D (Qt 4.7.2 64-bit version) provided by the Neuron Stitcher website, and it worked. Then I ran the Neuron Stitcher using the same test data with the Vaa3D (Qt 4.8.6 64-bit version), and the program crashed as well. We have recompiled the plugin of the Vaa3D (Qt 4.8.6 64-bit version), and it works now.

[b]Solution:[/b]
Attached is the recompiled file with the Vaa3D (Qt 4.8.6 64-bit version), you can replace the original file with it directly.
(original file: "C:/Users/USER/Downloads/Vaa3D_V4.001_Windows_MSVC_64bit/Vaa3D_V4.001_Windows_MSVC_64bit/plugins/neuron_stitch/1_stitchers")

The link below is some demo videos. If you are interested, you can check these videos below for more information.
http://cobweb.cs.uga.edu/~hanbo/4press/neuronStitcher/

I hope my answer is helpful to you. If you have any questions, please feel free to ask me.

Good luck!

Need help with neuron stitcher plugin

marinka88 — Wed, 14 Apr 2021 18:26:02 GMT

Hello everyone!
I work in neuroanatomy lab at UCLA. I am trying to stitch two parts of a neuron. I have two .swc files generated via Neutube. One is 102Kb and the other is 15Kb. For stitching, I am using the neuron_stitcher plugin, the auto version. However, when it starts running the program crashes.
Here is the log from the command prompt:
C:\Users\USER\Downloads\Vaa3D_V4.001_Windows_MSVC_64bit\Vaa3D_V4.001_Windows_MSVC_64bit>vaa3d_msvc.exe
[vaa3d_msvc.exe]
"C:/Users/USER/Downloads/Vaa3D_V4.001_Windows_MSVC_64bit/Vaa3D_V4.001_Windows_MSVC_64bit"
Searching in ./plugins ......
Searching ./plugins done.
"C:/Users/USER/Downloads/Vaa3D_V4.001_Windows_MSVC_64bit/Vaa3D_V4.001_Windows_MSVC_64bit"
Starting Vaa3D version checker...
Vaa3D MainWindow::dropEvent
" drop Url data: /C:/Users/USER/Documents/3D stuff/Vaa3d/2020-03-16_09.52.39_Cux2-MORF3_ML02-4_TAM-50x1_V5(647)_06A-Rec2_Stitched_103_360_480_1779_2389_3699.Edit.swc"
" the file to open: [C:/Users/USER/Documents/3D stuff/Vaa3d/2020-03-16_09.52.39_Cux2-MORF3_ML02-4_TAM-50x1_V5(647)_06A-Rec2_Stitched_103_360_480_1779_2389_3699.Edit.swc]"
V3dR_MainWindow::V3dR_MainWindow =====================================
"3D View []"
V3dR_GLWidget::V3dR_GLWidget ========================================
V3dR_MainWindow::connectSignal with V3dR_GLWidget
V3dR_GLWidget::initializeGL
GLformat: (version = 0x1f07f) (samples double-buffer stereo plane overlay = 4 1 0 0 0)
GLformat: (r g b a = 8 8 8 8) + (depth stencil accum = 24 8 64)
V3dR_GLWidget::choiceRenderer
Renderer::Renderer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Renderer_gl1::Renderer_gl1
OpenGL 2.0 (or higher) is available!
[OK] OpenGL Shading Language is available!
Renderer_gl2::Renderer_gl2
V3dR_GLWidget::settingRenderer
V3dR_GLWidget::preparingRenderer
Preparing 3D View
10
30
Renderer_gl1::cleanData
Renderer_gl1::setupData
Down-sampling to 512x512x256
data4dp = 0x0 (start 0x0x0_0_0, size 0x0x0_0_0)
rgbaBuf = 0x0 (0x0x0_0_0)
data box in original image space @ (0 0 0)--(-1 -1 -1)
data4dp_to_rgba3d ............................................... cost time = 0 sec
70
Renderer_gl2::initialize (2)
Renderer_gl1::initialize (1)
Renderer::initialize (0)
Renderer_gl1::cleanObj
Renderer_gl1::loadObj
Renderer_gl1::cleanVol
Renderer_gl2::cleanStreamBuffer
Renderer_gl1::loadVol
BoundingBox surface (1 1 1)--(-1 -1 -1)
BoundingBox default (0 0 0)--(0 0 0)
Renderer_gl2::cleanShader
Renderer_gl2::loadShader
+++++++++ shader for Surface Object
Load shader: ":/shader/obj_fragment.txt"
Load shader: ":/shader/lighting.txt"
Load shader: ":/shader/color_vertex.txt"
Load shader: ":/shader/lighting.txt"
GL Error #1281(invalid value) in File ..\3drenderer\glsl_r.cpp at line: 362
+++++++++ shader for Volume texture2D
Load shader: ":/shader/tex_fragment.txt"
+++++++++ shader for Volume texture3D
Load shader: ":/shader/tex_fragment.txt"
GL Error #1281(invalid value) in File ..\3drenderer\glsl_r.cpp at line: 362
+++++++++ GLSL shader setup finished.
Renderer_gl2::initColormap
100
++++++++++++ customEvent: 4
V3dR_GLWidget::customEvent( ? )
( QEvent_InitControlValue )
V3dR_MainWindow::initControlValue
GL texture compression supported, enable texture compression function
GL shading language supported, enable volume colormap function
"V3dR_MainWindow::changeEvent, ActivationChange-> 3D View [C:/Users/USER/Documents/3D stuff/Vaa3d/2020-03-16_09.52.39_Cux2-MORF3_ML02-4_TAM-50x1_V5(647)_06A-Rec2_Stitched_103_360_480_1779_2389_3699.Edit.swc]"
++++++++++++ customEvent: 2
V3dR_GLWidget::customEvent( ? )
( QEvent_OpenFiles )
Renderer_gl1::loadObjectListFromFile
-------------------------------------------------------
---------------------read 2396 lines, 2396 remained lines
Loading Neuron structure C:/Users/USER/Documents/3D stuff/Vaa3d/2020-03-16_09.52.39_Cux2-MORF3_ML02-4_TAM-50x1_V5(647)_06A-Rec2_Stitched_103_360_480_1779_2389_3699.Edit.swc
50
Renderer_gl1::updateBoundingBox surface (-4.63779 2.78438 3.56776)--(1296.29 1292.92 248.448)
Renderer_gl1::updateBoundingBox default (-4.63779 2.78438 3.56776)--(1296.29 1292.92 248.448)
++++++++++++ customEvent: 1
V3dR_GLWidget::customEvent( ? )
( QEvent_Ready )
-------------------------------------------------------------- Ready
V3dR_MainWindow::dropEvent
" drop Url data: /C:/Users/USER/Documents/3D stuff/Vaa3d/2020-03-16_09.52.39_Cux2-MORF3_ML02-4_TAM-50x1_V5(647)_06A-Rec2_Stitched_250_380_1402_2600_1550_2646.Edit.swc"
Renderer_gl1::loadObjectFromFile (url)
open file: "C:/Users/USER/Documents/3D stuff/Vaa3d/2020-03-16_09.52.39_Cux2-MORF3_ML02-4_TAM-50x1_V5(647)_06A-Rec2_Stitched_250_380_1402_2600_1550_2646.Edit.swc"
-------------------------------------------------------
---------------------read 352 lines, 352 remained lines
Loading Neuron structure C:/Users/USER/Documents/3D stuff/Vaa3d/2020-03-16_09.52.39_Cux2-MORF3_ML02-4_TAM-50x1_V5(647)_06A-Rec2_Stitched_250_380_1402_2600_1550_2646.Edit.swc
50
Renderer_gl1::updateBoundingBox surface (-6.11092 2.78438 -24.4137)--(1296.29 1292.92 248.448)
Renderer_gl1::updateBoundingBox default (-6.11092 2.78438 -24.4137)--(1296.29 1292.92 248.448)
runPluginInterface2_1 ... 0x1fb19efbff0
search for 3D windows
match and select 3D windows
number of markers = 0
number of markers = 0
done with runPluginInterface2_1().
already run! done status=1
number of markers = 0
rescale in stacking direction
align in stacking direction
search candidates
init neuron 0: cand: 2
init neuron 1: cand: 2
start find cliques
init neuron 0: 3clique: 0
init neuron 1: 3clique: 0
start match cliques
found 0 pair of cliques
start global search
global match: 1 matched points found; energy: 0
update makers: 4
Renderer_gl1::updateBoundingBox surface (-527.925 2.78438 3.56776)--(1296.29 1603.04 371.32)
Renderer_gl1::updateBoundingBox default (-527.925 2.78438 3.56776)--(1296.29 1603.04 371.32)
number of markers = 4
Fail to run the V3dR_GLWidget::updateLandmark() function.
number of markers = 4
Fail to run the V3dR_GLWidget::updateLandmark() function.
The pixel map size is 0 0 (for invalid imagedata)
The pixel map size is 0 0 (for invalid imagedata)
The pixel map size is 0 0 (for invalid imagedata)
cur layout=0000000000000000
MainWindow::createMdiChild *** workspace->windowList: () += XFormWidget(0x1fb2140ecc0)
size hint=1184 1153 min size hint=1184 1048
XFormWidget::setCurrentFileName: "neuron_stitcher_zoom_view"
MainWindow newImageWindow: "neuron_stitcher_zoom_view"
V3d_PluginLoader newImageWindow: XFormWidget(0x1fb2140ecc0)
V3d_PluginLoader setImage: 0x1fb2140ecc0 0x1fb2478a450
MainWindow setImage now: XFormWidget(0x1fb2140ecc0) 0x1fb2478a450
[000001FB2478A8F0]
now in the function setImageData() line=4886.
channel 0 min=[0] max=[0]
channel 1 min=[0] max=[0]
ChannelTable::linkXFormWidgetChannel CDim=2
CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 succeed in setting up image data.
XFormWidget::setCurrentFileName: "neuron_stitcher_zoom_view_processed"
MainWindow setLandmark: XFormWidget(0x1fb2140ecc0) 0xf9417fac28
CTU_3 Qt has caught an exception thrown from an event handler. Throwing
exceptions from an event handler is not supported in Qt. You must
reimplement QApplication::notify() and catch all exceptions there.
Catch an exception at the main application level. Basically you should never see this. Please click Ok to quit and send the error log to the Vaa3D developers to figure out the problem.
QPainter::end: Painter ended with 3 saved states

Some timesaving tips on manual tracing by Vaa3D

Lingli Zhang — Fri, 02 Apr 2021 12:28:49 GMT

Hello

Since I have been used Vaa3D in manual neuron tracing and worked with experienced annotators for half a year, I'd like to share some short keys which was frequently used and proved to be time-saving and effective.

1）Alt-N: Highlight the drawing curves without breakpoints.
This function could be used in the process when you were to be finished annotation and helped you to quickly check whether there were missing segments/breaking point or not.
2) Alt-N+D: Delete series of drawing curves highlighted.
This function could be very helpful in the manual tracing correction process, it can delete all segments under the wrong branch.
3) Alt-T+shift / Alt-D +shift: Retype/Delete multiple neuron-segments in batch. Drawing a circle to circulate the segments to be deleted by holding on the shift key.

Hope that helpful, and anticipate to be supplemented.

Advanced axon tracing techniques and analysis

Shane Simo — Wed, 30 Sep 2020 20:12:50 GMT

Hi folks,
I have been using Vaa3D for several months. I primarily use Vaa3D to trace axons. I am very competent with the basics, but I want to make sure I get good with some of the advanced concepts too. I have a few questions:
1.) Is there a comprehensive, advanced guide specifically for axon/neurite tracing? I want run my axon through a quality control of sorts. It would be helpful if there was a tutorial for the neurontoolbox funciton menu.
2.) I haven't been able to find a Sholl analysis in Vaa3D and I've been having trouble getting SNT to work on FIJI. I saw in the forum that you folks were working on a Sholl analysis plugin. What's the status of that? Is it available to users? I would like to avoid using SNT if possible.
3.) Are there any other useful pluggins for analysis of axons?
4.) I saw this question pop up a couple of times in the forum, but how do I know what the scalebar means on the 3D viewer? I have a voxel size of about 200nm * 200nm * 500nm from my confocal collection. How does that translate to Vaa3D? I saw that Vaa3D is in voxel space. What does that mean?

Thank you for your help! I really enjoy using Vaa3D so far, but I want to become a Vaa3D expert!
Shane Simon

Alignment of different sMRI data

Sadia Kamal — Sun, 13 Oct 2019 12:14:08 GMT

Dear all

My work is related to CC shape measurement. For that I am using already segmented CC data from OASIS. How can I align all the segmented CC (or its original sMRI data). The data is from around 400 subjects ?

Thanks in advance

Best Regards
Sadia

Parameters of APP2 for Command line of Vaa3d

Roozbeh Farhoodi — Thu, 26 Sep 2019 23:49:10 GMT

Hi,
I am using the command line to run app2 to trace neuron with vaa3d. I follow this page: https://github.com/Vaa3D/Vaa3D_Wiki/wiki/commandLineAccess.wiki
Based on the help, to call app2 in terminal we should write:

>> vaa3d -x plugin_name -f app2 -i -o -p vaa3d -x plugin_name -f app2 -i -o -p [inmarker_file [channel [bkg_thresh [b_256cube [b_RadiusFrom2D [is_gsdt [is_gap [length_thresh [is_resample][is_brightfield][is_high_intensity]]]]]]]]]

where -p is for the parameters. When I run it without parameters, it chooses default values and works well. But when I set the parameters and put inmarker_file=NULL, it does not work.

Would appreciate your help.

RE: Light-sheet users and experience with automatic tracing?

James Wilsenach — Mon, 01 Jul 2019 11:49:23 GMT

I have since found out that there was a memory limiting issue in that 32GB of RAM was insufficient to perform distance transforms on a 1500*1500*600 pixel image. After re-running results have much improved and APP2 seems to be the best choice (most detailed reconstruction) for my LSFM data.

RE: Light-sheet users and experience with automatic tracing?

James Wilsenach — Tue, 04 Dec 2018 17:45:04 GMT

Hi Hanchuan

Thanks for your interest, I am running the CentOS v3.458 version of Vaa3D on a Fedora machine. My problems with APP2 has been that the method under default or auto thresholding parameter settings seems to produce either one huge node in the former case or an overly thick arbor with some incorrect branching and a number of thin, spurious branches that all seem to line-up in parallel (screenshot of swc and max Z projection attached). Perhaps this could be improved by increasing the threshold further? Adding markers has not proven successful yet and has lead to arbors that ignore branches entirely and only go through marker points. I am trying to avoid manual curation however so this is not too concerning. I am not expecting perfect results from APP2 with my test image however as the soma of the single cell I am imaging is just out of field.

For other plugins I often received plugin failed to run or other messages. For instance, when attempting to run TreMap I get:

open file [/..._tmp/group_one.raw_group_1.swc] failed!

Or when using one of the distance field methods I get for instance:

The plugin fails to run [Other method 2: dfs]. Check your plugin code please.

Or running Rivulet 2:

Making Gradients of Time Crossing Map...The plugin fails to run [tracing]. Check your plugin code please.

The plugins appear to be intact and available (github, pre-compiled version). Per another post on the site I had to re-name the libstdc++.so.6 file to default to the system version. Could other incompatibilities like this be the source?

http://nitrc1.rssing.com/browser.php?indx=63431137&item=155

Here is a link to the input tif file:

https://drive.google.com/drive/folders/1C3O2EMMTt9lAdHc-mBgEhwsAkeUMIbvD?usp=sharing

Thanks in advance for any help!

Kind regards
James