SWC_BATCH_CHECK v.1.0

• Batch validation of directory containing SWC files
• Ensures structures are correctly connected
• Fix structures with zero size diameter
• Corrects index sequence
• Reports on missing data
• Ensures file starts with soma
• Returns basic statistics for each file

Installation

1. Download and extract the SWC_BATCH_CHECK.zip file
   tar -xzvf SWC_BATCH_CHECK.zip or
   git clone https://github.com/dohalloran/SWC_BATCH_CHECK.git

2. cd SWC_BATCH_CHECK

3. chmod +x install.sh

4. ./install.sh or sudo ./install.sh

   • if dependency fails you can try using --force
   • on MacOS Majave you will need Xcode, CommandLineTools, and headers
   • Install Xcode and then the CommandLineTools from Xcode
   • For headers: xcode-select --install
   • and then: open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

perl Makefile.PL  
make  
make test  
make install  

• might need to sudo make install depending on permissions

Usage

To run, add the following into a driver script:

use SWC_BATCH_CHECK;
use Modern::Perl;

my $app = SWC_BATCH_CHECK->new_with_options();
$app->run_SWC_BATCH_CHECK(); 

from the command-line:

perl driver.pl --d ./my_SWC_directory
#see command flags below

Command Line Arguments

Flags

#path to input directory containing SWC files (required)
       --d ./my_SWC_directory/
#provide corrections to soma that are not connected to other soma       
       --soma
#checks that axons are properly connected to more axon or soma       
       --axon
#ensures apical dendrites are connected to apical dendrite or soma
       --apic
#same as --apic flag except for basal dendrite
       --basal
#converts radius = 0 entries to that of its parent's radius
       --rad
#compression of output SWC directory
       --zip
#print flag options to stdout
       --help 

References

1. SWC Format Specification

2. SWC+ Plus Format Specification

3. Stockley, E. W., Cole, H. M., Brown, A. D. and Wheal, H. V. (1993) A system for quantitative morphological measurement and electronic modelling of neurons: three-dimensional reconstruction. Journal of Neuroscience Methods, 47, 39-51

Testing

SWC_BATCH_CHECK was successfully tested on:

• Microsoft Windows 7 Enterprise ver.6.1
• MacOSX Mojave ver.10.14.5
• Linux Mint ver.19 Tara

Contributing

All contributions are welcome.

Support

If you have any problem or suggestion please open an issue here.

License

GNU GENERAL PUBLIC LICENSE