Posted by
ctrueden on
Aug 12, 2016; 5:28pm
URL: http://imagej.273.s1.nabble.com/SOLVED-Simple-multi-stacks-to-individual-images-tp5017009p5017012.html
Hi Philippe,
> We "just" want to split (stack to image) all of them into numerated
> individual images (from 1, the first image of the first stack, to x,
> the last one of the last stack).
Why not use the Bio-Formats command line tools? Specifically, the bfconvert
command:
https://www.openmicroscopy.org/site/support/bio-formats5.1/users/comlinetools/conversion.htmlFrom the documentation:
> Images can also be written to multiple files by specifying a pattern
> string in the output file. For example, to write one series,
> timepoint, channel, and Z section per file:
>
> bfconvert /path/to/input output_series_%s_Z%z_C%c_T%t.tiff
>
> %s is the series index, %z is the Z section index, %c is the channel
> index, and %t is the timepoint index (all indices begin at 0).
Regards,
Curtis
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Curtis Rueden
LOCI software architect -
http://loci.wisc.edu/softwareImageJ2 lead, Fiji maintainer -
http://imagej.net/User:RuedenDid you know ImageJ has a forum?
http://forum.imagej.net/On Fri, Aug 12, 2016 at 5:13 AM, pognonec <
[hidden email]> wrote:
> Hi List,
>
> First, I am not familiar with ImageJ macro writing, while not being
> completely ignorant.
>
> We have *lots* of .ome.tif stacks (4GB each). These stacks were generated
> (by MicroManager) from scanning multi-well plates in a single channel, a
> single z, a single t. These stacks are in a single folder.
> We "just" want to split (stack to image) all of them into numerated
> individual images (from 1, the first image of the first stack, to x, the
> last one of the last stack).
> That sound quite simple, but I have not been able to write a macro doing
> just that...
> I have looked in previous posts, but what I found had to do with splitting
> channels, and did not help in this case.
>
> Any help or hint would be appreciated!
>
> Thanks,
> Philippe
>
>
>
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