Stitching LSMs with channels in separate files.

Posted by Niko Ehrenfeuchter on Dec 16, 2014; 4:59pm
URL: http://imagej.273.s1.nabble.com/Stitching-LSMs-with-channels-in-separate-files-tp5010964.html

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
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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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