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help > SWC files from APP2 - multiple numbers in 'type' column
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Apr 18, 2018 01:04 PM | esteves5 - University of Toronto
SWC files from APP2 - multiple numbers in 'type' column
Hi!
I used Neuron-APP2 to trace a neuron and my resulting SWC file has multiple numbers listed in the 'Type' column. I expected to see a single digit number ranging from 1 to 5 in the 'Type' column.
Does anyone know why this is occurring? And how to fix it? Attached is my SWC file.
Also, why are 2 files created from APP2: *_ini and *_app2 ?
The issue I am referring too is for the _app2 swc file, the _ini file doesn't have this issue, but the _ini file has many more points and the z dimension is constrained to whole integer numbers. Is the *_ini file the "initial" trace file prior to down sampling? When I load the *_ini file into Vaa3d no graph is produced.
Thank-you! Any information is welcome! Or if there is any documentation for the different tracing algorithms that have plug-ins for Vaa3d, that would be great!
I used Neuron-APP2 to trace a neuron and my resulting SWC file has multiple numbers listed in the 'Type' column. I expected to see a single digit number ranging from 1 to 5 in the 'Type' column.
Does anyone know why this is occurring? And how to fix it? Attached is my SWC file.
Also, why are 2 files created from APP2: *_ini and *_app2 ?
The issue I am referring too is for the _app2 swc file, the _ini file doesn't have this issue, but the _ini file has many more points and the z dimension is constrained to whole integer numbers. Is the *_ini file the "initial" trace file prior to down sampling? When I load the *_ini file into Vaa3d no graph is produced.
Thank-you! Any information is welcome! Or if there is any documentation for the different tracing algorithms that have plug-ins for Vaa3d, that would be great!
Apr 18, 2018 04:04 PM | Zhi Zhou
RE: SWC files from APP2 - multiple numbers in 'type' column
For your questions:
1. The type information in APP2 results is not "real" neuron type, it just represents the tracing order information. You can manually change these type information.
2. *_ini.swc is an initial result, and *app2.swc is the final result. More information, you can check APP2 paper: http://home.penglab.com/papersall/docpdf/2013_BIOINFO_app2.pdf
3. All tracing algorithms information can be found from here (https://github.com/BigNeuron/BigNeuron-W...)
1. The type information in APP2 results is not "real" neuron type, it just represents the tracing order information. You can manually change these type information.
2. *_ini.swc is an initial result, and *app2.swc is the final result. More information, you can check APP2 paper: http://home.penglab.com/papersall/docpdf/2013_BIOINFO_app2.pdf
3. All tracing algorithms information can be found from here (https://github.com/BigNeuron/BigNeuron-W...)