> Hi Jacob,
>
> > 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?
>
> Let's wait to see what Wayne says. I am guessing he will change ImageJ
> somehow to adjust for this situation.
>
> In the meantime, feel free to try the Groovy script I posted earlier.
>
> 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 1:38 PM, Jacob Keller <
[hidden email]>
> wrote:
>
> > 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> >
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
Locked
UnBinnable.tif (1M)