Fiji grid/collection stiching/position from file/defined by image metadata

Dear All,
it is a beginner to Fiji. I 'd like to use the grid stiching plugin, for tiled stacks. MAnually it works well, I want to, however, automate the process. My metadata file that contains the tile position is sometimes corrupted, so I can not use it. However it is the only way, because the x-y structure of my tiles is always different. Could you tell me how shall I build up a custom metadata file, if I know the relative tile positions (not the concrete coordinates, it is in the corrupted metadata file.)

Thanks in advanece

Hi @Levente,

Welcome to the forum.

You’re using this plugin for grid/collection stitching right?

If that’s correct, read up on the details of that plugin here. Specifically, if the metadata are not correct / reliable, you can create a TileConfiguration file. From that same page, it gives you an example TileConfiguration, it looks like this:

# Define the number of dimensions we are working on
dim = 3
# Define the image coordinates (in pixels)
img_73.tif; ; (0.0, 0.0, 0.0)
img_74.tif; ; (409.0, 0.0, 0.0)
img_75.tif; ; (0.0, 409.0, 0.0)
img_76.tif; ; (409.0, 409.0, 0.0)
img_77.tif; ; (0.0, 818.0, 0.0)
img_78.tif; ; (409.0, 818.0, 0.0)

If you can make a file like that, then you’re all set,

Dear John, thanks for the helpful feedback. Indeed, this is one way, and a right way, if the microscope stage movement is reliable enough. I do not know, if alignment corrections at the borders are done, if the input coordinates are not completely correct. By definition the tile overlap is 10% by the microscope I use, so I can calculate the coordinates. This is theoretical.

Many Thanks