How to Display Your ImageJ Data in the Juyter Notebooks¶

This tutorial will show you how to display and visually manipulate your image data

In [1]:

//load ImageJ
%classpath config resolver imagej.public https://maven.imagej.net/content/groups/public
%classpath add jar /home/gabe/code/imagej/imagej-common/target/imagej-common-0.27.0-SNAPSHOT.jar
%classpath add jar /home/gabe/code/gselzer/imagej-notebook/target/imagej-notebook-0.3.0-SNAPSHOT.jar
%classpath add mvn net.imagej imagej 2.0.0-rc-67

//create ImageJ object
ij = new net.imagej.ImageJ()

Added new repo: imagej.public

Out[1]:

net.imagej.ImageJ@15b66095

Let's say that you used an Op within the notebooks:

In [6]:

input = ij.scifio().datasetIO().open("http://imagej.net/images/cat.jpg")

sigmas = [3, 3, 0]
gaussed = ij.op().run("gauss", input, sigmas)

null

[INFO] Populating metadata

Out[6]:

null

All you have to do to display your output is give Jupyter the reference to your imageJ object on the last line of the cell:

In [7]:

gaussed

Out[7]:

ImageJ has given Jupyter the ability to display any RandomAccessibleInterval or DatasetView as is using this method. However there is only scratching the surface of what we can visually modify. Let's use the view method of ImageJ-notebook to turn our RandomAccessibleInterval into a DefaultDatasetView:

In [8]:

dataset = ij.notebook().view(gaussed)

println(dataset)

Out[8]:

In [9]:

import net.imagej.display.ColorTables
import net.imagej.axis.Axes

dataset.setColorTable(ColorTables.RED, 0)
dataset.setColorTable(ColorTables.GREEN, 1)
dataset.setColorTable(ColorTables.BLUE, 2)
view.rebuild()
view

java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
	at net.imagej.display.DefaultDatasetView.setColorTable(DefaultDatasetView.java:196)
	at net.imagej.display.DatasetView$setColorTable.call(Unknown Source)
	at this cell line 5
	at com.twosigma.beakerx.groovy.evaluator.GroovyCodeRunner.runScript(GroovyCodeRunner.java:94)
	at com.twosigma.beakerx.groovy.evaluator.GroovyCodeRunner.call(GroovyCodeRunner.java:59)
	at com.twosigma.beakerx.groovy.evaluator.GroovyCodeRunner.call(GroovyCodeRunner.java:32)

NOTE: the rest of this notebook will showcase the displaying features that will be cemented in ImageJ/imageJ-notebook. Once these are finished, add them!¶

In [ ]: