vaa3d / vaa3d_wiki Goto Github PK

hello, first i want to say va3d is a very powerful tool to process medical images！！！ thanks！！！

recently i am using vaa3d to trace vessel with "plug-in" "neuron tracing" "MOST tracing" function.
it is perfectly satisfy my needs! but i have a lot of data , so maybe it's better to understand MOST and write code to auto trace.

but i can not find any information about MOST tracing online, unless its writer jingpengwu(jpwu@CBMP).
can you give me some knowledge about MOST? or where can i get it ?

thank you very much !

When using teraconverter I am trying to convert a TIFF file with 251 z-planes, but teraconverter sets the z-planes on 126. The rest of the resolutions are correct except the z-planes. Is 126 z-planes the max or is something else happening? It would be great if someone could help! If more information is needed please ask.

Thanks in advance.

Requested by Yun Wang.

1. manually set a radius adjustable landmark to separate 1 neuron tree into 2 neuron trees, the color of each separated neuron tree can be assigned at this time;

2. after completing one part of neuron tracing, the color can be assigned at this time;

3. be able to connect the multiple selected traced segments into a single neuron tree; current issue of the automated method is going to create some unnecessary incorrect connections;

4. be able to autotrace neurons in a small local window;

5. support clicking a "incomplete end (ie) point" from the "ie" list and the 3D window will go to the field of view of 1:1 resolution corresponding block; current function will go back to a coarser resolution block;

6. (nice to have) global lower resolution whole mouse brain rendering / navigation map.

in particular the executable gives this documentation, which doesn't map to the web.

Also In particular, the --halve option isn't explained what integers map to which options?

USAGE:

./teraconverter -s= [-d=] [--mdata_fname=]
[--ch_dir=] [--depth=]
[--height=] [--width=]
--sfmt= --dfmt=
[--resolutions=] [--halve=]
[-f=] [--info=] [--noprogressbar]
[--verbose] [--V0=] [--V1=]
[--H0=] [--H1=] [--D0=]
[--D1=] [--isotropic] [--parallel]
[--makedirs] [--metadata] [--algorithm=] ...
[-p] [--imin_plugin=]
[--imin_plugin_params=]
[--imout_plugin=]
[--imout_plugin_params=]
[--dsfactor=] [--timeseries]
[--libtiff_uncompress]
[--libtiff_rowsperstrip=] [--] [--version]
[-h]

Where:

-s=, --src=
(required) Source file / root directory path.

-d=, --dst=
Destination root directory path.

--mdata_fname=
File containing general metadata of the image.

--ch_dir=
subdirectory to store the channel (single channel in tiled 4D format
only).

--depth=
Slice depth.

--height=
Slice height.

--width=
Slice width.

--sfmt=
(required) Source format ("Vaa3D raw"/"Vaa3D raw (series, 2D)"/"Vaa3D
raw (tiled, 3D)"/"Vaa3D raw (tiled, 4D)"/"TIFF (3D)"/"TIFF (series,
2D)"/"TIFF (tiled, 2D)"/"TIFF (tiled, 3D)"/"TIFF (tiled, 4D)"/"TIFF
(unstitched, 3D)"/"HDF5 (BigDataViewer)"/"HDF5 (Imaris IMS)"/"Mapped
Volume")

--dfmt=
(required) Destination format ("Vaa3D raw (series, 2D)"/"Vaa3D raw
(tiled, 3D)"/"Vaa3D raw (tiled, 4D)"/"TIFF (series, 2D)"/"TIFF (tiled,
2D)"/"TIFF (tiled, 3D)"/"TIFF (tiled, 4D)"/"HDF5
(BigDataViewer)"/"HDF5 (Imaris IMS)")

--resolutions=
Resolutions to be produced. Possible values are [[i]...] where i = 0
,..,5 and 2^i is the subsampling factor.

--halve=
Halving method (mean/max, default: mean).

-f=, --outFmt=
Voxel format (graylevel or RGB (default)/intensity.

--info=
File path of the info file to be saved.

--noprogressbar
Disables progress bar and estimated time remaining

--verbose
set verbosity to maximum level (to be activated ONLY for debugging)

--V0=
First V vertex (included).

--V1=
Last V vertex (excluded).

--H0=
First H vertex (included).

--H1=
Last H vertex (excluded).

--D0=
First D vertex (included).

--D1=
Last D vertex (excluded).

--isotropic
Generate lowest resolution with voxels as much isotropic as possible.
Use this flag when the high resolution image has highy anistropic
voxels

--parallel
Does not perform side-effect operations during the merge step. Use
this flag when more merge steps are launched in parallel

--makedirs
Creates the mdata.bin file of the output volume.

--metadata
Creates the directory hierarchy.

--algorithm= (accepted multiple times)
Forces the use of the given algorithm.

-p, --pluginsinfo
Display plugins informations

--imin_plugin=
Plugin that manages the input image format. Available plugins are:
{"tiff2D", "IMS_HDF5", "tiff3D"}. Default is "auto".

--imin_plugin_params=
A series of parameters "param1=val,param2=val,..." to configure the
input image plugin (see --pluginsinfo for the list of accepted
parameters)

--imout_plugin=
Plugin that manages the output image format. Available plugins are:
{"tiff2D", "IMS_HDF5", "tiff3D"}. Default is "auto".

--imout_plugin_params=
A series of parameters "param1=val,param2=val,..." to configure the
output image plugin (see --pluginsinfo for the list of accepted
parameters)

--dsfactor=
Dowsampling factor to be used to read the source volume (only for
serie of 2D slices).

--timeseries
The input is a time series.

--libtiff_uncompress
Configure libtiff library to not compress output files (default:
compression enabled).

--libtiff_rowsperstrip=
Configure libtiff library to pack n rows per strip when compression is
enabled (default: 1 row per strip).

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

I'm attempting to build vaa3d on mac osx version 10.14.6. When I do so, I receive a warning

warning "This version of Mac OS X is unsupported"

along with many other errors, which I assume are due to this issue. Which versions of osx are supported for vaa3d?

I am trying to start running with the appropriate binary distribution.

I get the error:

./Vaa3D-x: error while loading shared libraries: libQt6OpenGLWidgets.so.6: cannot open shared object file: No such file or directory

I see in the README:

NOTE!!
if you encounter

• If you find that you have problems with opengl not loading, try adding the Qt
  libraries to the environment variables

How do I add Qt libraries to the environment variables? That is, how can I find my Qt installation and know what to add.

Thanks in advance for your assistance.

Hello I have been trying to utilise the swc_to_maskimage (a very useful tool thanks)
I have a recent issue, I get the error message: "the plugin fails to run [swc_to_maskimage] check your plugin code."

I have no other error information to begin debugging, all I can say is that the swc file I am trying to convert, reads in and displays with no problems if I just open it.

Any help much appreciated, I am running Vaa3D v3.2 on windows 11.

Hi, I am trying to run the paraconverter to convert from 2D TIFF series to IMS file. When running I get a "Bad Magic Number" error. I am using Python 3.7 (Anaconda download) for other reasons. Could it be that it was compiled in 2.7 and this causes the error? If so could I get the .py file and compile it in 3.7 and use this?

Thanks!

The links on TeraConverter download page are 404'd by Dropbox: https://github.com/Vaa3D/Vaa3D_Wiki/wiki/TeraConverter#download

Hi,

I was looking through the docs and the repos to see if the tool can do automatic centerline detection? I noticed that "centerline" was mentioned in some code files but not sure if it can be used to perform automatic centerline detection in CT scans. Please let me know.

Also, thank you for sharing this software with the open source community!

For output, either in teraconverter or paraconverter mode, is it possible to force an exact tile-size based on height/width/depth, even if there are some small edge tiles? The default seems to load balance the output into tiles that are approximately the same size, using the input height/width/depth as rough guidelines.

My use case is a secondary step to create a precomputed cloud-volume -- or any format viewable by neuroglancer. My current understanding is that the parallel uploading of such a volume would benefit from exact tiling, preferably with dimensions in powers of two.

Hey, I meet some questions about TIFF. I have already configured and generate a file named ALL_BUILD.vcxproj. Then open it with VS2013 and generate solution. But when configure and build Vaa3D, I found lot of header file about tiff bring compile error. Such as missing header file tiffconf.h and redefine. So can you tell me how can I do?
By the way, lots of file are same in v3d_external and vaa3d_tools, so if you didn't define path the file operated, should I operate both file v3d_external and vaa3d_tools?

User Manual cannot be downloaded.

Is there any instructions on building with MSVC 2019 64bit

Hi, for testing data 5D (x-y-z-c-t) image series data visualization - A series of image-stacks, each corresponding to a time point. Can be loaded using the Vaa3D "Import" function. you actually uploaded TwoColorCelegansWiggling.zip, can you upload the 5D testing data again? thanks so much!

Hi, I downloaded the linux binaries (CentOS) and got an error because it looks for libpng12.

I am using Debian 10 and libpng12 has been abandoned; apparently there are some security vulnerabilities there.

I understand that distro-specific issues are not a problem with Vaa3D, but is there a reason to continue to use libpng12 instead of libpng16?