http://imagej.273.s1.nabble.com/Shortening-Z-Stacks-tp5019255p5019269.html
Okay, but it seems like binning should be a pretty commonly-used operation,
especially in the realm of hyperstacks. Is there something that can be done
> 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> >
>
> --
> ImageJ mailing list:
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