atlasguided_stranno_partial.wiki

Check out location

	svn co https://svn.janelia.org/penglab/projects/vaa3d_tools/released_plugins/v3d_plugins/celegans_seganno

Usage

func

seganno
help

   Usage : v3d -x atlasguided -f seganno -i <inimg_file> <inmarker_file> <inatlas_file> <incell_file> [<incell2_file>] 
               -o <outatlas_file> <outseglab_file> 
               -p <refchannel> <ratio> <fgthresh> <initemp> <minitemp> <ann_rate> <iter> <useCell2>

     inimg_file      name of input image file
     inmarker_file   name of input marker file
     inatlas_file    name of input atlas file
     incell_file     name of input interesting cell file
     incell2_file    name of input secondary interesting cell file. If useCell2 is 0, this field is empty
     outatlas_file   name of output atlas file
     outseglab_file  name of output seg-label file
     refchannel      channel number, r: 1, g: 2, b: 3, default 2
     ratio           downsampling ratio, default 4
     fgthresh        fg thresh factor, default 3
     initemp         initial temperature, default 20
     minitemp        minimal temperature, default 0.2
     ann_rate        annealing rate, default 0.95
     iter            iter per temperature, default 1
     useCell2        whether to import secondary interesting cell names from file, 1: yes, 0: not. default 0

   e.g. v3d -x atlasguided -f seganno -i inimg_file.raw inmarker_file.marker inatlas_file.apo incell_file.txt 
            -o myoutatlas.apo outseglab.raw -p 2 4 3 20 0.2 0.95 1 0