Correct 3D drift virtual

Hi, I’m trying to use the Correct 3D drift plugin on a data set that is around 9gb and contains 2 channels. Can’t run it all in RAM, it gives an error after finishing and never produces the corrected image. According to the paper on this plugin, you can use the virtual option to get around this. I check the virtual box and select a directory, but after it has corrected the image it again gives an error, this time saying “savefile is not specified”.

Anyone know why it does this and how I can get around it?

EDIT: Correction, the error it puts out is: NameError: global name ‘FileSaver’ is not defined

@David, that means that the FileSaver Java class was not imported. It’s a bug in the Correct_3D_drift.py script that was fixed a while ago, but apparently the corrected file wasn’t uploaded to the Fiji updater yet.

We can ask @hinerm or @ctrueden to upload it when they find time.

As a workaround in the meantime, you can click on Plugins > Registration > Correct 3D drift while holding down the Shift key: this will open the file in the script editor, and you can adjust line 12 yourself to fix it. Then simply click Run in the script editor to run the adjusted script.

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Thanks, will try it out now!

OK, I just uploaded the four Python scripts—including Correct_3D_drift.py—which had been updated on Fiji master a few months back, but never uploaded to the update site.

This sort of skew will disappear once we switch away from manual uploads, in favor of Jenkins doing it directly from master. (Or in the case of ImageJ core: directly from each release version tag.)

Just to conclude: The fix worked wonderful, could stabilize huge datasets. Thanks alot!

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