[ome-users] Mirror before stitching?

[Sam Lord]

OK, I've tried with a more recent nightly build of Micro-Manager, and the stitching appears to work well (when I flip y). There must have been some issue reading the metadata before. Thanks for all your help, everybody!

-Sam

On Jun 20, 2013, at 3:12 PM, Sam Lord <sjlord at berkeley.edu> wrote:

> Dear Bjorn,
> 
> Thanks for the input. I still think that if each image was flipped in y, the whole thing would stitch correctly in LOCI. Or is my spatial reasoning off?
> 
> I have been unable to use the Grid/Collection Stitch plugin in the manner that you suggest, because it doesn't import a single image stack when you ask it to import by snake-by-rows: it wants a series of files. Instead, it simply tiles the first frame of the stack over and over.
> 
> I suspect that the plugin doesn't like the format of stage position in my metadata. Or something.
> 
> FYI, I am using a relatively up-do-date version of Micro-Manager for image acquisition.
> 
> Thanks for your help, all. But this just doesn't seem to be working for me.
> 
> -Sam
> 
> 
>> Hi Sam,
>> 
>> 
>> when I look at your attachment, I am pretty sure, that the top row should be 
>> on the bottom of the stitched image, the second row from top should be the 
>> second from bottom and so on. So there is no error in your metadata, nor in 
>> the plugin, its just the interpretation of the 0,0 coordinate. ImageJ should 
>> interprete 0,0 on left top of an image, your software might use left bottom. 
>> So no flipped Y-axis in images, just different order of tiles. Trie to fix it by 
>> telling the plugin to use row by row, left & up.
>> 
>> 
>> Best Björn