Re: Image5D bug?

Posted by Jacob Keller-2 on Aug 24, 2017; 6:21pm
URL: http://imagej.273.s1.nabble.com/Image5D-bug-tp5019256p5019268.html

Right, it does work...sort of: it only outputs one time point. What I want
is timelapses of each z-slice all on the same x-y plane, to see
simultaneously what's happening at all z-levels. The normal "make montage"
command apparently only works for one time point, whereas the image5D
command accommodates the time dimension and therefore makes the sort of
movie-montage I want. Is it difficult to upgrade the native command to
allow this?

Jacob

On Thu, Aug 24, 2017 at 11:48 AM, Curtis Rueden <[hidden email]> wrote:

> Hi Jacob,
>
> > I get the error msg "5D hyperstacks are not supported."
>
> It will work if you use the "Image > Hyperstacks > Hyperstack to Stack"
> command first.
>
> 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 10:32 AM, Jacob Keller <[hidden email]>
> wrote:
>
> > I get the error msg "5D hyperstacks are not supported." Pls find attached
> > MCVE (same as other post.) This also happens when I get rid of one
> channel,
> > so it's only 4D.
> >
> > Jacob
> >
> > On Thu, Aug 24, 2017 at 10:49 AM, Curtis Rueden <[hidden email]>
> wrote:
> >
> > > Hi Jacob,
> > >
> > > The Image5D plugin, while currently part of Fiji, is not actively
> > supported
> > > [1].
> > >
> > > Is there some reason that ImageJ's built-in support for 5D hyperstacks,
> > > along with the "Make Montage..." command, cannot accomplish what you
> > need?
> > >
> > > The following macro creates a 16-bit montage of two images without
> using
> > > Image5D:
> > >
> > > run("Blobs (25K)");
> > > run("16-bit");
> > > run("Clown (14K)");
> > > run("16-bit");
> > > run("Images to Stack", "method=[Copy (center)] name=Stack title=[]
> use");
> > > run("Make Montage...", "columns=2 rows=1 scale=1");
> > >
> > > Regards,
> > > Curtis
> > >
> > > [1] http://imagej.net/Image5D; see right-hand sidebar
> > >
> > > --
> > > 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 6:05 PM, Jacob Keller <[hidden email]>
> > > wrote:
> > >
> > > > I have been using the nice capabilities of image5D, but there seem to
> > be
> > > a
> > > > couple of problems. My procedure is to split multichannel .czi xyzct
> > > stacks
> > > > into individual channels, stack-to-image5D, then montage. I noticed
> > some
> > > > strange behaviors in so doing:
> > > >
> > > > -when I make a montage, it is output as RGB, even though the input is
> > 8-
> > > or
> > > > 16-bit. Not too terrible, since it's easy enough to convert to 8-bit
> > from
> > > > there, although it's a shame to lose the 16-bit depth, and it seems
> > like
> > > > something funky is going on.
> > > >
> > > > -the last frame in the timelapse montages are always black
> > > >
> > > > -Contrast is weird: when I do not click "copy contrast" the images
> are
> > > > output way too bright, and it's not just the contrast setting. When I
> > do
> > > > click "copy contrast," sometimes things are fine, sometimes the
> > > intensities
> > > > (not just contrast settings) make discrete jumps inexplicably.
> > > >
> > > > Can you help me out here?
> > > >
> > > > 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
>

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