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saalfeldlab / paintera

GNU General Public License v2.0
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request: provide example Fiji Export N5 -> Paintera #429

Open dbock opened 3 years ago

dbock commented 3 years ago

I have Paintera running via Anaconda on a Mac laptop. I'd like to try it out on some data openable in Fiji. A reasonable workflow seems to be to "Export as N5" in Fiji (per https://github.com/saalfeldlab/n5-ij#export-n5), then either open directly in Paintera, or by using paintera-convert to-paintera (per https://github.com/saalfeldlab/paintera).

However after a few attempts I don't find the right set of parameters. A worked example in the documentation for this operation would be helpful.

GenevieveBuckley commented 2 years ago

I've been able to convert raw data to N5 using the Fiji plugin and have then successfully opened it in paintera.

Unfortunately, I haven't been able to do the same for label data (was just about to open an issue asking for help here too). I've tried a number of different ways without success, including editing the attributes.json files to try and better match the labels spec, and converting my data to HDF5 with Fiji and then trying to use the paintera-conversion-helper (no luck, it doesn't seem to recognise the dataset name contained in the HDF5 file).

Perhaps @hanslovsky can expand on how the specification should be met? I appreciate the detail included in https://github.com/saalfeldlab/paintera/pull/81 but am struggling to figure out how to apply it.

hanslovsky commented 2 years ago

@GenevieveBuckley I am not an active maintainer for Paintera anymore. @cmhulbert might have some insight.