Extended Depth of Field Plugin

Posted by Robert Baer on Apr 28, 2006; 5:35pm
URL: http://imagej.273.s1.nabble.com/different-results-using-ImageStatistics-and-Menu-Analyze-Measure-command-tp3702965p3702968.html

I have a small stack (~6 frames) of RGB fluroescent images that I tried the
Extended Depth of Field pluggin on.  I used the 'Easy Mode'.  In the initial
pass, I used the 'Fast' setting' on the quality slider and got a rapid
result.

I then cranked the slider up to 'high' quality and repeated the run.  The
progress bar showed one bar and did not progress from there over the next 30
min.  I got a couple more bars on the medium setting and then it seemed to
not progress.  At this point, I increased ImgagJ memory (from I think 300
Mb) to 1000 Mb and the medium setting worked like a charm.  The high setting
seemed still to stall out, but I think I got more than 1 bar on the progress
indicator before it stalled.  When it stalls there is no indicator, and the
memory shown by the Extended Depth of Field Plugin shows higher numbers than
the memory monitor for ImageJ.  On 'medium high' it progressed to 7
completion bars with 1000 Mb of memory for ImageJ, the plugin reports using
~300 mb and this number continues to fluxuate, but the ImageJ memory monitor
claims only 78 Mb (7%) and this number also fluxuates.

First am I correct that it is really stalled?  If so, this leads to some
additional questions:

1.  When I increased ImageJ memory to 1699Mb it would no longer start the
Java machine so I guess this is a limitation.  The memory dialog seems to
suggest ImageJ start-up will be okay up until 1700 Mb.  What exactly is the
memory limit for ImageJ or is it OS and machine dependent?

2.  Is there a way to figure out how much memory is required for the
extended depth of field plug-in?  Am I right that it is stalled when the
progress bar doesn't move for an hour or so (given that the intial bars
appeared in well less than a minute)?  Are there any suggestions for using
the Expert Mode to avoid this 'stall phenomenon' and still get an idea of
what the 'high quality' rendering looks like.

3.  Finally, the stack slider disappears during the process, so if I cancel
the plug-in the image has no slider.  If I duplicate the stack, the
duplicate stack has a slider again.  Any idea what is going on here?  Is
this a plug-in issue or an ImageJ issue.

Machine: 2.4 GHz Pentium 4 CPU with 1Gb memory.  Windows XP    Java
1.5.0_06b05  ImageJ 1.36b
Current config file:
    C:\PROGRA~1\ImageJ\
    C:\Program Files\Java\jre1.5.0_06\bin\javaw.exe
    -Xmx1000m -cp ij.jar;C:\PROGRA~1\ImageJ\ij.jar ij.ImageJ


Thanks for any insights,
Rob Baer