README.md

wmc_imagej

Authors: Gerhard Burger, Steven Wink

Work in progress, feel free to edit

Installation

Make sure you use Fiji with ImageJ2, the ImageJ that ISSC installs may not work!

• Install WMC Segment in ImageJ

  Download DImageSVN_.jar and place it in your ImageJ plugin directory. You should be able to use WMC Segment from Plugins > Analysis > Segmentation > WMC Segment. You can use this to determine the optimal settings for batch mode.

• Download WMC_batch.ijm by saving it as WMC_batch.ijm (make sure it ends with .ijm and not .txt, it doesn't matter where you save it).

Usage

The WMC_batch.ijm file cannot be installed as a macro, but must be run as script, which can be done in the following ways:

• (Recommended) Using the macro editor

  • Open ImageJ and go to Plugins > Macros > Edit... (or use the [ keyboard shortcut).
  • Open the WMC_batch.ijm file and click Run (bottom left)

• Using the commandline:
   Use the syntax described here (NB running with --headless doesn't work since WMCSegment requires a gui). Example uses:

  ~/opt/Fiji.app/ImageJ-linux64 --run /home/gerhard/WMC_batch.ijm 'paths="/data/gerhard/example_dir",suffix="tif",quit=true'
  

  or for multi files/folders

  ~/opt/Fiji.app/ImageJ-linux64 --run /home/gerhard/WMC_batch.ijm 'paths=["/data/gerhard/example_dir/test1.tif","/data/gerhard/example_dir/test2.tif"],quit=true'
  

  The quit=true option is to quit ImageJ after the job is done.

• Using R:

  From Linux:

imageDir <-  '/home/callegarog/examples/ImageExpressTests/test'
parameters <- paste( "\", pattern=\"", pattern, "\", suffix=\"", suffix)
system(paste("~/Fiji.app/ImageJ-linux64 --ij2 --run ", macroDir, "/WMC_batch.ijm 'paths=\"",
           imageDir, parameters, "\"'", sep=""))

  From Windows:

setwd(fijiDir)
parameters <- paste( "paths=", shQuote(imageDir, type = c("sh")),
                     ",pattern=", shQuote(pattern, type = c("sh")))
system2('ImageJ-win64.exe', args = c('--ij2', '--run', "macros/WMC_batch.ijm",
                                     parameters)) 

Notes:*

• The output folder (if set) does not copy the directory structure of the input folders, everything will be dumped in the same output folder, so files with the same names will probably be overwritten.