Re: ROI manager question

[dpoburko]

Hi All,

  This is a question for those folks with an indepth understanding of
the inner workings of ImageJ. ImageJ does some pretty cool things in a
very speedy fashion. So in comparison, it seems to be rather sluggish
and loading and deleting large lists (>~1000) of ROIs. Can anyone tell
me why this is, and if their is anyway to improve this?

Many thanks,
Damon

--
Post Doctoral Fellow
Tsien Lab, Molecular&  Cellular Physiology
Stanford University

[Bill Mohler]

I've been wondering about this as well.  I think a lot of the time lag
may actually be in zipping and unzipping the separate ROIs from the
files.  Has anyone tried saving ROIs without the zipping steps?

Bill

On 8/24/11 6:24 PM, Damon Poburko wrote:

> Hi All,
>
>    This is a question for those folks with an indepth understanding of
> the inner workings of ImageJ. ImageJ does some pretty cool things in a
> very speedy fashion. So in comparison, it seems to be rather sluggish
> and loading and deleting large lists (>~1000) of ROIs. Can anyone tell
> me why this is, and if their is anyway to improve this?
>
> Many thanks,
> Damon
>

[Rasband, Wayne (NIH/NIMH) [E]]

On Aug 24, 2011, at 6:24 PM, Damon Poburko wrote:

> Hi All,
>
>  This is a question for those folks with an indepth understanding of
> the inner workings of ImageJ. ImageJ does some pretty cool things in a
> very speedy fashion. So in comparison, it seems to be rather sluggish
> and loading and deleting large lists (>~1000) of ROIs. Can anyone tell
> me why this is, and if their is anyway to improve this?

This is a Mac vs PC issue. ROI Manager delete operations are 100 times slower on PCs. The trick for speeding things up on a Windows PC is to use batch mode. This test macro runs 300 times faster in batch mode.

  if (isOpen("ROI Manager")) {
     selectWindow("ROI Manager");
     run("Close");
  }
  start = getTime;
  setBatchMode(true);
  roiManager("Open", getDirectory("home")+"RoiSet.zip");
  print("count: "+roiManager("count"));
  roiManager("delete");
  print((getTime-start)/1000);

To get the 300 times speedup, the ROI Manager window must be closed when the macro enters batch mode.

-wayne