Question about imagej

[penningavery]

I am interested in using some ImageJ plugins to process some images from a python image processing pipeline. Has this been tried with JavaBridge and if so, how did it go?

For image processing applications in general, any pointers for using JavaBridge? Is the data transfer between numpy and java fast enough for image data? Thank you for your help.

[LeeKamentsky]

CellProfiler has code to bridge between ImageJ and Python. I would look at this release here: https://github.com/CellProfiler/CellProfiler/tree/2.1.1/imagej

for some clues. It might be easier to start clean and use the more modern JClassWrapper to get at the machinery to run plugins. In any case, it can definitely be done and there's a lot of synergy between ImageJ and Numpy.

[penningavery]

Hello,

Thanks very much for the pointers to the code. It's great that the core machinery looks to be there. I completely agree about the potential synergy between ImageJ and numpy and will post back with any successes on that front. Cheers.

On Mon, Nov 28, 2016 at 1:31 PM, LeeKamentsky [email protected] wrote:

CellProfiler has code to bridge between ImageJ and Python. I would look at this release here: https://github.com/CellProfiler/CellProfiler/ tree/2.1.1/imagej

for some clues. It might be easier to start clean and use the more modern JClassWrapper to get at the machinery to run plugins. In any case, it can definitely be done and there's a lot of synergy between ImageJ and Numpy.

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