Re: Shortening Z-Stacks

Posted by ctrueden on Aug 24, 2017; 3:46pm
URL: http://imagej.273.s1.nabble.com/Shortening-Z-Stacks-tp5019255p5019266.html

Hi Jacob,

Thanks, that helps.

It looks like the logic in the Binner class which handles hyperstacks is
commented out for some reason:

https://github.com/imagej/ImageJA/blob/v1.51p/src/main/java/ij/plugin/Binner.java#L76-L77

That also explains why it works when there is only one timepoint, since
IIRC, XYZT data constitutes a "hyperstack" but XYZ data does not.

So I'd call this a bug.

Here is a Groovy script which calls the hyperstack binning method directly:

#@ImagePlus image
#@int(label = "Z shrink factor", value = 2) zshrink
#@output ImagePlus result
import ij.plugin.Binner
result = new Binner().shrinkHyperstackZ(image, zshrink as int)

It appears to work in my tests, but be warned that that code might have
been commented out for a good reason -- e.g. to avoid bugs. So caveat
emptor.

Hopefully Wayne will have more insight into this.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Aug 24, 2017 at 10:24 AM, Jacob Keller <[hidden email]>
wrote:

> Got it--those guidelines make a lot of sense, and will try to follow them
> in the future. I've attached a really-minimized data set (1 MB) hereto for
> an MCVE. Binning, interestingly enough, does work in xy, but not z. When
> this data set is cut to one timepoint, z-binning works, so there might be
> some confusion between z/t. Maybe binning should ask explicitly for all
> (xyzt? maybe even c too?)
>
> Jacob
>
> On Thu, Aug 24, 2017 at 10:45 AM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Jacob,
> >
> > > The bin command is not working on them, perhaps because they are
> > > timelapses. Is this potentially a bug?
> >
> > It would help greatly to have a Minimal, Complete, Verifiable Example
> > (MCVE) illustrating the issue. For guidance, see this article:
> > http://imagej.net/Bug_reporting_best_practices
> >
> > Regards,
> > Curtis
> >
> > --
> > Curtis Rueden
> > LOCI software architect - https://loci.wisc.edu/software
> > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> > Did you know ImageJ has a forum? http://forum.imagej.net/
> >
> >
> > On Wed, Aug 23, 2017 at 5:54 PM, Jacob Keller <[hidden email]>
> > wrote:
> >
> > > Dear Imagers,
> > >
> > > I have some .czi z-stack timelapses which are 40-60 slices in z, but it
> > > would be nice to merge them down to, say, 10-20 slices by binning
> > adjacent
> > > slices. The bin command is not working on them, perhaps because they
> are
> > > timelapses. Is this potentially a bug?
> > >
> > > All the best,
> > >
> > > Jacob Keller
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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