Best Method for using ImageJ Plugins in python?

Usage & Issues
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#1

Hi Everyone,

I wanted to ask the community what the best method is for accessing ImageJ plugins in python. I know that you can write scripts/macros through jython, but it would be better for our workflow to use a different package. Does anyone have experience using ImageJ plugins with the PyImageJ package? Specifically, I am trying to utilize the MIST stitching plugin (https://github.com/usnistgov/MIST) and I am wondering what may be the most accessible way to access such a plugin in custom python scripts. Thanks for your help!

Edit: I have found that using the run_plugin feature with PyImageJ works great! If there are any other cool solutions that people have found I would love to hear them.

#2

Hi,

Yes, This is a good first trial -

in your python script -

import imagej
import scyjava
import jgo

scyjava.config.add_option(ā€™-Xmx6gā€™)
ij = imagej.init(ā€˜C:\Programs\ImageJ2\Fiji.appā€™, headless=False) # Look up the documentation for this command onlineā€¦
ij.py.run_plugin(ā€œplugin nameā€)

Search either imagej.init() or ij.py.run_plugin() and you will find examplesā€¦
obviously, the .init() command should be modified to where your imagej2 resides or an official version that the script will download.
you will also need JRE 8 and pip install pyimagejā€¦

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