"Grid/Collection stiching" plugin & Channels

Dear all,

I’m “struggling” (a bit) with the “Grid/Collection stitching” plugin.

I have 3x3 grid with 2ch and 3z.
I get 3 different results by stitching the tiles of the ch1, of the ch2 or containing both.

“Grid/Collection stitching” plugin.

  • Type : Position from file
  • Order : Defined by TileConfiguration
  • Default options + Compute overlap

The documentation page mentions that "The plugin is not built to register different channels to each other. However, if you want to do that anyways simply convert channels into time-points … “

Since, I got 3 different results I assume that when both channel are presents, it doesn’t compute the stitching from channel 1 but for a mix of channel 1 and 2?

Since stitching of the 2nd channel is the best one (others have one, or more, misaligned tile(s) ) for the moment the workaround solution is the one recommended on the doc page, ie swapping channels and time-points, and using ch2 as the first time-point.

Do others ImagJists think it would be nice if the user could select an option for the stitching to either use :

  • 1 particular channel
  • an Average of them (or another operation)

Thank you for your feedback,


You can download the full dataset (all the tested images, tile configuration files, resulting images)

or a lighter version (only the 9pos x (2ch+3z) + TileConfiguration file)

On multi-channel images, an average of all channels is used. It says so at some places in the source code/javadoc (admittedly a bit hard to spot):

You could also perform the stitching on the separated channel 2 images, and re-use the TileConfiguration.registered.txt (without re-computing the overlap) for the channel 1 images in a second step. That depends on your workflow.

Regarding a user-facing option to select a specific channel for the computation of phase correlation, I don’t think it’s available from the UI, but you might be able to do so using script calls into the API… maybe @StephanPreibisch has some recommendations here.

On a related note, did you try BigStitcher already? I’m not sure, but it might actually have the functionality you’re looking for.

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