Grid/collection stitching

[Lara Linden-2]

Hello all,

I am trying to use the FIJI Grid/Collection stitching plugin to stitch confocal z-stacks acquired in Micromanager with filename convention 1770 2DA_MMStack_Pos_{xxx}_{yyy}.ome.tif. The image grid is acquired in a row by row, left & up order.

The deprecated stitch directory with images (unknown configuration) option can occasionally stitch these stacks correctly.

The filename defined position option can open but cannot correlate the tiles. The first tile is represented multiple times in the stitching image output, and z-stacks are sometimes stacked incorrectly on top of each other in z.

The positions from file: defined by image metadata option output seems to include all the tiles, but their configuration is incorrect. I have attached the log and console files and screenshot from running this option.

Thanks for your help!

Lara Linden

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