Posted by
Brian Willkie-2 on
Apr 28, 2008; 6:08pm
URL: http://imagej.273.s1.nabble.com/advice-on-running-ImageJ-headless-tp3696386.html
Hello,
I need a command line application to process ~17000 images, tracking
particles and collecting (at least) particle-id, centroid, and area,
(and possibly standard deviation, min/max, and mean within the
particle,). I also need to format and write the results to disk, doing
all with no gui/ no additional interaction once the command-line
options are set.
I've found a little information on Headless ImageJA from the wiki:
http://imagejdocu.tudor.lu/imagej-documentation-wiki/faq/how-do-i-run-imagej-without-a-graphics-environment-headless/?searchterm=no%20guiGiven the size of this project, I'd like to solicit some advice on
how to proceed:
1. Can I run headless ImageJA only in batch mode (i.e. do I have to
work with macros?), or can I use headless ImageJA to build my own
application using the ImageJ API?
2. I've had the most success in particle-tracking with MTrack2.
However MTrack2 won't provide the area (nor standard deviation,
min/max, nor mean). I don't mind adapting the code myself, but I'd
like to know if this is the best (only?) option?
If the answers to 1 and 2 are yes, then I assume the way to proceed is:
1. adapt the MTrack2 code for my own plugin to be called in a macro
following the examples in the ImpProps and Image5D_Extensions plugins.
2. Write a macro that calls my adapted particle-tracking plugin.
3. Run ImageJ from the command line with headless.jar in the
classpath, the -batch flag, and call my macro.
Does this sound accurate? Am I missing something? Is there a better
way, or is this the way to go?
Thanks,
Brian Willkie