help > APP2 batch processing
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Jan 18, 2018 03:01 PM | max_92
APP2 batch processing
I want to use the APP2 algorithm to trace neurons from .tif stacks.
When I open a single stack in Vaa3d i can select the plugin
(Vaa3D-Neuron2 auto-tracing) and specify the parameters. For
batch processing I want use the command line acces of the plugin. I
can process a single image with default paramerters with the
command:
'./start_vaa3d.sh -x /home/max/Documents/Master_Thesis/Vaa3D_Ubuntu_64bit_v3.200/plugins/neuron_tracing/Vaa3D_Neuron2/libvn2.so -f app2 -i /home/max/Documents/Master_Thesis/2017_11_03/ALM/ALM1.tif -o outfile.swc
When trying to specify the parameters I add:
'-p [NULL [0 [60 [0 [1 [0 [0 [3 [0][0][0]]]]]]]]]'
at the end as specified in the function help ('./start_vaa3d.sh -x /home/max/Documents/Master_Thesis/Vaa3D_Ubuntu_64bit_v3.200/plugins/neuron_tracing/Vaa3D_Neuron2/libvn2.so -f help').
I tried different syntaxes for the parameter (changing the brackets, using stings around the values or the whole thing etc.) but the plugin does not use my specified parameters.
Can anyone help?
'./start_vaa3d.sh -x /home/max/Documents/Master_Thesis/Vaa3D_Ubuntu_64bit_v3.200/plugins/neuron_tracing/Vaa3D_Neuron2/libvn2.so -f app2 -i /home/max/Documents/Master_Thesis/2017_11_03/ALM/ALM1.tif -o outfile.swc
When trying to specify the parameters I add:
'-p [NULL [0 [60 [0 [1 [0 [0 [3 [0][0][0]]]]]]]]]'
at the end as specified in the function help ('./start_vaa3d.sh -x /home/max/Documents/Master_Thesis/Vaa3D_Ubuntu_64bit_v3.200/plugins/neuron_tracing/Vaa3D_Neuron2/libvn2.so -f help').
I tried different syntaxes for the parameter (changing the brackets, using stings around the values or the whole thing etc.) but the plugin does not use my specified parameters.
Can anyone help?
Jan 18, 2018 05:01 PM | Zhi Zhou
RE: APP2 batch processing
For parameter inputs. please directly use: -p NULL 0 60 0 2 0 0 3 0
0 0
Jan 29, 2018 10:01 AM | max_92
RE: APP2 batch processing
I have another question concerning batch-processing with APP2.
There is the option to do an automatic soma detection (-p NULL) or
to input a marker file with a starting point (-p ). I intend to use
the algorithm without soma-detection. I generated the marker-file
in vaa3D by selecting a point (right-click) and then pressing 'm'
to save a marker. Then I exported the marker as an .apo-file and
used the resulting file as the first parameter. According to the
algorithm the marker is loaded but it is invalid. What is the
correct format of the inmarker-file for neuron-tracing without
soma-detection?
PS: Here is what the .apo file generated by vaa3D looks like:
0, 0, landmark 1,, 17,727,1019, 255.000,38.083,59.559,882.000,33589.000,,,
PS: Here is what the .apo file generated by vaa3D looks like:
0, 0, landmark 1,, 17,727,1019, 255.000,38.083,59.559,882.000,33589.000,,,
Jan 29, 2018 05:01 PM | Zhi Zhou
RE: APP2 batch processing
Please directly use the saved marker file as the input, which is a
*.marker format.
Jan 30, 2018 11:01 AM | max_92
RE: APP2 batch processing
This does not work for me. The only way I found to export landmarks
from Vaa3D was to select a point by right-clicking and creating a
landmark by pressing 'm', then exporting the landmark using "File
-> Export -> Export landmarks to pointcloud (.apo) file". The
only other option "Plug-In -> marker_utilities ->
marker2others -> Save markers to SWC format" crashes my program.
In the Vaa3D Documentation it says:
"You can export the markers' location and annotation, as well as the statistics, by either saving the respective landmarks into a plain text file (.marker file, which has the simple CSV - comma separated values - format), or export it as an .APO file (pointcloud file, also in the CSV format)."
As I cannot export a .marker file from Vaa3D I don't know the exact format needed (I did check multiple csv variants, including changing the .apo suffix to .marker).
Can you tell me (1) How to export a .marker file from Vaa3D or (2) the exact format of a marker file that is recognized by the APP2 algorithm?
Thanks :)
In the Vaa3D Documentation it says:
"You can export the markers' location and annotation, as well as the statistics, by either saving the respective landmarks into a plain text file (.marker file, which has the simple CSV - comma separated values - format), or export it as an .APO file (pointcloud file, also in the CSV format)."
As I cannot export a .marker file from Vaa3D I don't know the exact format needed (I did check multiple csv variants, including changing the .apo suffix to .marker).
Can you tell me (1) How to export a .marker file from Vaa3D or (2) the exact format of a marker file that is recognized by the APP2 algorithm?
Thanks :)
Jan 30, 2018 02:01 PM | Zhi Zhou
RE: APP2 batch processing
In 3D view, right click on the marker, you will find an option to
save the marker directly.