Re: Stitching LSMs with channels in separate files.

Posted by ctrueden on Dec 16, 2014; 5:31pm
URL: http://imagej.273.s1.nabble.com/Stitching-LSMs-with-channels-in-separate-files-tp5010964p5010965.html

Hi Niko,

> Can we make the plugin write the config

The fact that it doesn't seems like a bug to me.

Maybe try changing the logic here:

https://github.com/fiji/Stitching/blob/Stitching_-2.0.1/src/main/java/plugin/Stitching_Grid.java#L502-503

To also write the file when the fusion method is set to "Do not fuse images
(only write TileConfiguration)".

And see how that works for you?

If you can get it working, file a PR and we can get it fixed upstream.

Regards,
Curtis

On Tue, Dec 16, 2014 at 10:59 AM, Niko Ehrenfeuchter <
[hidden email]> wrote:

>
> Dear all,
>
> we're facing the situation where one of our users acquired a lot of
> tilings on a Zeiss LSM but saved each channel in a separate .lsm file. So
> each file contains like 30 stacks (listed as "series" when opening them
> through BioFormats), but only single-channel.
>
> Stitching the channels individually using the Grid/collection stitching
> from Stephan Preibisch is pretty straightforward, as it can just use the
> stage coordinates via the "use positions from metadata" option.
>
> However, some of the channels are rather sparse and there the stitching
> results in quite different coordinates compared to the "base" channel.
> First I thought, fine, lets just use the TileConfiguration.registered.txt
> usually created by the plugin when operating on given coordinates. This way
> we could use the "good" channel to do the registration and then just apply
> it to the others. However, I had to learn that in the case of stage
> coordinates coming from the LSM metadata, this file is not written.
>
> Next, I tried to use the coordinates printed to the Log window by the
> plugin after the registration step, but I couldn't find out how to specify
> sub-series in a TileConfiguration file (or if this is possible at all).
>
> Any ideas? Can we make the plugin write the config, or can we turn the log
> output into something re-usable as input config?
>
> Thanks
> Niko
> --
> Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University of
> Basel | Klingelbergstr. 50/70 | CH-4056 Basel
> Phone: [phone] | [hidden email] |
> www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
>
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>

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