real_time_numpy_to_imagej.py

# real-time visualization of numpy arrays in ImageJ
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# Installation:

# 1. conda create -n pyimagej -c conda-forge pyimagej openjdk=8 
# 2. conda activate pyimagej
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import imagej
import numpy as np
import time
import scyjava as sj

ij = imagej.init('/home/beams/USER2BMB/Software/Fiji.app',mode='interactive')
ij.ui().showUI()
ImagePlus = sj.jclass('ij.ImagePlus')

#initialize a window
array1 = np.random.rand(32, 32)
image1 = ij.py.to_java(array1)
ij.ui().show(image1, cmap='gray')
imp1 = ij.py.active_imageplus()

while True:
   time.sleep(1)
   #initialize a new ImagePlus for new data
   array2 = np.random.rand(32, 32)
   array2[16,:] = 0
   array2[:,16] = 0
   imp2 = ij.py.to_java(array2)
   imp2 = ij.dataset().create(imp2)
   imp2 = ij.convert().convert(imp2, ImagePlus)
   #place the new ImagePlus in original ImagePlus
   imp1.setImage(imp2)