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Re: Image5D bug?

Posted by Jacob Keller-2 on Aug 24, 2017; 3:32pm
URL: http://imagej.273.s1.nabble.com/Image5D-bug-tp5019256p5019265.html

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
>
--
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UnBinnable.tif (1M) Download Attachment