[ome-users] Mirror before stitching?

[Sam Lord]

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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