Stitching LSMs with channels in separate files.

[Niko Ehrenfeuchter]

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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[ctrueden]

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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Niko Ehrenfeuchter]

Hi Curtis,

On 16.12.2014 18:31, Curtis Rueden wrote:
> 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

thanks!

> 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?

in the end it was a bit more complicated as it was not possible to
specify sub-series in a TileConfiguration.txt file. However, I've
implemented the required parts and filed a PR [1] just some minutes ago.

Cheers
~Niko

[1] https://github.com/fiji/Stitching/pull/26

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