http://imagej.273.s1.nabble.com/Shortening-Z-Stacks-tp5019255p5019270.html
> especially in the realm of hyperstacks. Is there something that can
Let's wait to see what Wayne says. I am guessing he will change ImageJ
> 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
> in lieu of it? I have thought perhaps of making a macro which splits the
> timepoints into individual substacks, bins, then reassembles, but that
> seems a little clumsy...
>
> JPK
>
> On Thu, Aug 24, 2017 at 11:46 AM, Curtis Rueden <
[hidden email]> wrote:
>
> > 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:
http://imagej.nih.gov/ij/list.html> >
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>