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imagej / pyimagej

Use ImageJ from Python
https://pyimagej.readthedocs.io/
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No plugins loaded with imagej.init('sc.fiji:fiji') #82

Closed supersergiy closed 3 years ago

supersergiy commented 4 years ago

As far as I understood from documentation, initializing ij with imagej.init('sc.fiji:fiji') should load all the standard Fiji packages. However, when I attempted to run it only 1 JAR was loaded (Added 1 JARs to the Java classpath.) and I was unable to load classes from TrakEM2 package.

The same code works when given a path to the local Fiji installation, but it would be great if imagej.init('sc.fiji:fiji') would work.

imagejan commented 4 years ago

See https://github.com/imagej/pyimagej/issues/36.

I think this is fixed on master. @supersergiy how did you install pyimagej?

ctrueden commented 4 years ago

We need to release a new Fiji with all the latest components. In the meantime, see if imagej.init('sc.fiji:fiji+net.imagej:imagej-legacy:0.37.4') works any better?

ctrueden commented 3 years ago

In my hands today, imagej.init('sc.fiji:fiji') works and initializes with Fiji version 2.1.1, which includes imagej-legacy 0.37.4.

@supersergiy Please rm -rf ~/.jgo and try again. And if it still doesn't work for you, please reopen this issue!