CARE in Fiji macros

Hi all,

I’ve been training a model for 3D denoising using the online jupyter examples on my own data and wanted to apply it to a time-lapse afterwards. Since CARE on Fiji is not yet time-lapse friendly I thought to prototype a batch processing by recording the command launch of CARE in Fiji and make a macro feed CARE 1 time point at a time.
Thanks to you spending time on making it recordable it works very nicely (and results are very convincing!), but I couldn’t figure out how to stop a GUI asking me to provide the model URL from popping up at every new timepoint… Is there something I missed?

I’ll certainly try again later in Jython or Python but it might be useful to offer this batching possibility to people who want to program it in macro since it is almost there.

Thanks again for the great work and documentation!

Sebastien

also, a couple details, trying to find my problem I’ve seen that some links at the bottom of the documentation page here could be updated:
the link
https://github.com/CSBDeep/CSBDeep_fiji/tree/master/src/main/java/mpicbg/csbd/commands
could be updated to
https://github.com/CSBDeep/CSBDeep_fiji/blob/master/src/main/java/de/csbdresden/csbdeep/commands/GenericNetwork.java

and the link
https://github.com/CSBDeep/CSBDeep_fiji/script
to
https://github.com/CSBDeep/CSBDeep_fiji/tree/master/script

@fjug

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If someone needs to run an hyperstack someday, I modified the jython script available here to handle hyperstacks automatically and process the whole timelapse.
Available here

Sebastien

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