Posted by
ctrueden on
Aug 24, 2017; 2:49pm
URL: http://imagej.273.s1.nabble.com/Image5D-bug-tp5019256p5019262.html
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/softwareImageJ2 lead, Fiji maintainer -
https://imagej.net/User:RuedenDid 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
>
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