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Hello,

I'm having trouble passing parameters to the APP2 plugin via the command line.

If I don't pass any parameters by not using the -p or /p then APP2 uses reasonable default parameters For example running: Vaa3D-x.exe /x vn2 /f app2 /i "C:\Users\Desktop\Peng V3D test data\neuron01.tif" /o "C:\Users\Desktop\Peng V3D test data\test.swc"
Results in:
##Vaa3D-Neuron-APP2 v2.621
#channel = 0
#bkg_thresh = 10
#length_thresh = 5
#SR_ratio = 0.333333 .... etc and a reasonable swc trace

However, when I add the /p command, APP2 switches to using different parameters, but not those specified in the /p string
Running: Vaa3D-x.exe /x vn2 /f app2 /i "C:\Users\Luke_H\Desktop\Peng V3D test data\neuron01.tif" /o "C:\Users\Luke_H\Desktop\Peng V3D test data\test.swc" /p [NULL [1 [10 [1 [1 [0 [1 [5 [1][0][0]]]]]]]]]
Results in:
##Vaa3D-Neuron-APP2 v2.621
#channel = 0
#bkg_thresh = -1
#length_thresh = 0
#SR_ratio = 0.333333
#is_gsdt = 0
#is_gap = 0
#cnn_type = 2 etc and a hyperbranched swc

This command is based on the information provided by Vaa3D-x.exe /x vn2 /f help
Is there a different way to pass the parameters? Or has something changed in APP2 since the last help information from this plugin was created?

I think this is a fantastic tool and hope there is an easy solution to this.

Many thanks!

Luke

I can't find this file at anywhere in this whole project.

../../../../vaa3d_tools/hackathon/PengXie/preprocess/pre_processing_main.h:46:68: 致命错误：..\..\MK\v3d_imgManagerMK\integratedDataStructures.h：没有那个文件或目录
#include "..\..\MK\v3d_imgManagerMK\integratedDataStructures.h"

I really need help,thank you very much!

As of af416b8 there were a bunch of my files in the profundo module. Then, after @qiangouyang pushed 03d6b74 these files went missing. Strangely, when I look at 03d6b74 it shows 11 changed files, but none of them are mine. Because of this, I don't know how to revert the deletions with git. @gnayuy

Hi,

I am trying to run this for neuronal reconstructions on Vaa3D (Windows 10), but I don't see it in the plug-ins.

I am very new to programming and all that, so I'm sure that I am missing something here.

-brainsick5ht

I was trying to use the RegressionTubularityAC ported in Bigneuron for automatic centreline detection on Ubuntu, since I like the paper and keen to see how it performs.

However the plugin .so file was not included in the released 3.2 version. The trained models and filters were included though.

When I tried to compile it I got the errors saying could not find -llbfgs and -lconfig++. It might be due to the .lai files attached with this plugin. I fixed by replacing the .lai files with the right .so files. Then I could compile the plugin without errors.

Both the training and testing failed silently with only a message The plugin fails to call [test]. Check your plugin code please. (This is shown normally when ITK fails within vaa3d due to unknown reason)

Has anyone successfully ever used this plugin with some work around?

Hi
I found a morphology with the following line at the end of the header:

# generated by Vaa3D Plugin neuron_connector

So I came here.

The first point of this file is:
1 3 0.000 0.000 0.0 0.5 0
which means that it's parent does not exist. In the SWC specs, the first point should have a parent ID equal to -1 (see https://www.sciencedirect.com/science/article/pii/S0165027098000910, https://neuromorpho.org/myfaq.jsp (in the What is SWC format? section) or https://neuroinformatics.nl/swcPlus/). So I guess there is an issue with this plugin (maybe only when there is no soma?).

Dataset consists of multichannel multiframe tiff files.Each frame is obtained at a deeper focal length of in-vivo tissue.We are looking to correct motion artifacts of brain images obtained by 2d photon microscopy on live mice at successive focal lengths along the axial plane. So, in summary, although we do not have a time scale right now(maybe in future),we are just looking to correct for motion artifacts within and between frames.
More formally,there are n tiff stacks. Each stack has Nimgs where each img is from a depth along the axial plane of the brain, n is the number of channels. Once motion corrected, we are looking to trace the dendrites belonging to a stack in 3d.
Can someone please advice how to use Vaa3d for this motion correction and image registration problem ?

In released_plugins/v3d_plugins/resample_swc/resample_swc_func.cpp there are two problems.
In the code

	QTextStream myfile(&file);
	myfile<<"# generated by Vaa3D Plugin resample_swc"<<endl;
	myfile<<"# source file(s): "<<fileOpenName<<endl;
	myfile<<"# id,type,x,y,z,r,pid"<<endl;
	for (V3DLONG i=0;i<lN.size();i++)

The endlines in this code are not being processed right for me.
I believe it is assuming that this is the stdlib endl rather than the QText endl. I think you should just be able to change it to Qt::endl and it should be fine.

A slightly more serious issue,
http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html
The specification here says that "Parent samples should appear before any child samples." This is not satisfied in the current incarnation. The graph should be sorted topologically before it is written to the file.

Thank you!

when I compile vaa3d_tools, it failed. according the tips, I guess that, maybe i have used a unmatched version of vaa3d_tools. so my question is :
which version (or git revision ) of vaa3d_tools should I use for matching v3d_external v3.20 ?

the version of v3d_external that I must use is v3.20(from https://github.com/Vaa3D/v3d_external/archive/refs/tags/v3.20.tar.gz)
the version of vaa3d_tools i try to use is v1.03（from：https://github.com/Vaa3D/vaa3d_tools/archive/refs/tags/imPreProcess_v1.03.tar.gz）

-----------bellowing, chinese language----------
我想使用的主库v3d_external的版本是v3.20（from：https://github.com/Vaa3D/v3d_external/archive/refs/tags/v3.20.tar.gz）。
我选用的vaa3d_tools是v1.03（from：https://github.com/Vaa3D/vaa3d_tools/archive/refs/tags/imPreProcess_v1.03.tar.gz）。
当我在linux上编译vaa3d_tools时，出现如下报错：

我怀疑是vaa3d_tools的版本与v3d_external v3.20不匹配，所以想请问下vaa3d_tools应该选用哪个版本？

Hi,
I read the Paper "SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology".

Can I request to have this dataset in this paper?

Thank you and regards,
Khoa