[ome-users] Mirror before stitching?

[Curtis Rueden]

Hi Sam,

> I've been having a lot of trouble getting the Fiji Grid/Collection
> Stitching plugin to operate how I want.

Thanks for the report. I am forwarding this thread to fiji-devel, which is
a better place to report issues with Fiji plugins such as Grid/Collection
Stitching.

> -If I deselect "compute overlap," I would expect the plugin to simply
> place the tiles where the stage position in the metadata claims it is.
> Instead, the output seems to not include most of the images.

Try reducing the overlap slider to 0. IIRC, it defaults to 10, and that
factor still applies even if you uncheck "compute overlap."

> -When I do select "compute overlap," the images often aren't placed
> anywhere near the right locations. For instance, it will output an
> irregular shape, when the fused image should be a rectangle.

There are various ways of tuning how it approaches the computation, but if
your stage coordinates are already very accurate, you probably don't need
the "compute overlap" feature anyway.

> I'm sure some of these issues result from a non-perfect pixel
> calibration and the fact that I did not include any overlap in my
> tiles when acquiring them.

Ah, yes. If you do not include any overlap, then the "Compute overlap"
feature will always fail. It relies on overlap between tiles to detect how
things should be laid out. Your only option when collecting fully
non-overlapping tiles is to uncheck "Compute overlap" and reduce the
overlap slider to 0. It should then lay them out exactly how you collected
them.

> However, the LOCI importer seems to not worry about that. Instead, it
> happy tiles my images. The only problem is that I can tell the images
> are flipped in the y direction.

Right, the LOCI importer will stitch your image *exactly* how the metadata
says, and cannot do anything else such as flip tiles inverted in Y. So I
suggest you try the Grid/Collection Stitching plugin again as I described
above. If you still cannot get it work, and are willing to post a sample
non-working dataset, we can investigate further.

Regards,
Curtis


On Wed, Jun 19, 2013 at 11:29 AM, Sam Lord <sjlord at berkeley.edu> wrote:

> Hi Curtis,
>
> I've been having a lot of trouble getting the Fiji Grid/Collection
> Stitching plugin to operate how I want. I'm asking it to select positions
> from file and instructing it to use the image metadata. Here are some
> issues I've found:
>
> -The color scheme does not import. Neither does some other metadata (e.g.
> pixel size).
> -If I deselect "compute overlap," I would expect the plugin to simply
> place the tiles where the stage position in the metadata claims it is.
> Instead, the output seems to not include most of the images.
> -When I do select "compute overlap," the images often aren't placed
> anywhere near the right locations. For instance, it will output an
> irregular shape, when the fused image should be a rectangle.
>
> I'm sure some of these issues result from a non-perfect pixel calibration
> and the fact that I did not include any overlap in my tiles when acquiring
> them. However, the LOCI importer seems to not worry about that. Instead, it
> happy tiles my images. The only problem is that I can tell the images are
> flipped in the y direction.
>
> Is there a way to "brainlessly" tile my images from metadata location AND
> flip y?
>
> -Sam
>
>
> On Jun 16, 2013, at 11:49 AM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>
> Hi Sam,
>
> We recently added an "invert Y axis coordinates" option (and one for X as
> well) to the Stitching plugins. Did you try that?
>
> The Fiji Grid/Collection Stitching plugin, in case you haven't tried it,
> uses Bio-Formats and is much more powerful than the BF Importer's basic
> stitching feature.
>
> Regards,
> Curtis
>  On Jun 16, 2013 12:01 PM, "Sam Lord" <sjlord at berkeley.edu> wrote:
>
>> Importing stacks from Micro-Manager works well using Bio-Formats
>> Importer, and the stacks option seems to read location directly from
>> metadata. The only issue I have is that my camera must be rotated 180
>> degrees, because the columns stitch together well, but each row is
>> upside-down.
>>
>> I tried importing the stack, flipping, exporting, then reimorting, but
>> something must have gotten lost in the metadata in that maneuver.
>>
>> Any chance there is a simple way to tell the stitching that the images
>> are flipped?
>>
>> -Sam
>>
>> _______________________________________________
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>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>
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