Re: Extended Depth of Field Plugin

Posted by Michael Herron on Apr 28, 2006; 7:26pm
URL: http://imagej.273.s1.nabble.com/different-results-using-ImageStatistics-and-Menu-Analyze-Measure-command-tp3702965p3702969.html

Rob,

Have you tried just using a maximum projection on these images? Works  
pretty good for fluor images.

Mike

On Apr 28, 2006, at 11:35 AM, Robert W. Baer, Ph.D. wrote:

> 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

Michael J. Herron,  U of MN, Dept. of Entomology
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