Manual lateral correction taken into account for stitching

[Bobafotz]

Hello,

I did some manual correction on the tile position in the "Stitching Explorer" window (2 tiles positions were completely inverted). After that, I launched the "Stitch dataset" command. Could you confirm me that the manual correction I did will be (at least roughly) take into account for the stitching process ?

Thank you !

[hoerldavid]

Hi @Bobafotz,

When we stitch a dataset, we do two things to speed up the process and make it more robust to correlations between unconnected images:

• We only compare images that are overlapping (according to the current registration, e.g. your manual correction)
• We only use the overlapping regions of two images to calculate the shift between them (this essentially constrains the automatic registration so that the overlap of the registered images will be >0 and <2overlap according to pre-registration/metadata). As this can lead to some errors if the metadata overlap is too small, the next version of BigStitcher, due to be released soon, will include the option to use the whole images for the calculation, at the cost of longer compute times and risk of correlations between distant parts of the images*

Furthermore:

• In the expert options, we also support stitching using the Lucas-Kanade algorithm, which essentially starts at the current location of the images and iteratively shifts them around until it converges to an optimal registration.
• If we cannot calculate shifts between all neighboring images, we will try to preserve the metadata/manually aligned location of "unconnected" tiles as well as possible using out 2-round global optimization.

I guess this is a long answer to a simple question, but the gist of it is: While our algorithms try to find an optimal registration regardless of the current image locations, there are may ways in which they implicitly take manual pre-alignment or metadata into account. While BigStitcher is quite robust and should work even with no metadata or pre-registrations, providing those will drastically speed up the process and also increase the chances of a successful alignment

Hope this helps and clarifies the situation somewhat! Don't hesitate to ask if you have further questions!

Best, David

[Bobafotz]

Hello David,

Thank you very much for the detailled answer, it did help me a lot and I hope it will help others. It is clear to me now. And again, you did a terrific job on this plugin, it worked like a charm, the stitching of (not good looking) datas is perfect. Thank you for this tool !

Have a good day,

Julien