ImageJ Tutorials and Demo

Welcome to the ImageJ tutorial series. These notebooks offer a hands-on series of lessons for learning ImageJ.

Feedback is very welcome! Please share your ideas on the ImageJ Forum!

Advanced extensions

  1. Creating a custom service (coming later)
  2. Customizing module execution (coming later)
  3. Creating a SCIFIO plugin (coming later)

ImageJ Demo

First, we spin up an ImageJ. For more details on how this works, see the Fundamentals of ImageJ notebook.

In [1]:
%classpath config resolver imagej.public https://maven.imagej.net/content/groups/public
%classpath add mvn net.imagej imagej 2.0.0-rc-71
ij = new net.imagej.ImageJ()
"ImageJ v${ij.getVersion()} is ready to go."
Added new repo: imagej.public
Out[1]:
ImageJ v2.0.0-rc-71 is ready to go.

Load some images

In [2]:
sourcePath = "https://imagej.net/images"
//sourcePath = System.getProperty("user.home") + "/data"
cells = ij.io().open(sourcePath + "/FluorescentCells.jpg")
mandrill = ij.io().open(sourcePath + "/baboon.jpg")
ij.notebook().display([["mandrill": mandrill, "cells": cells]])
[INFO] Populating metadata
[INFO] Populating metadata
[INFO] Populating metadata
[INFO] Populating metadata
Out[2]:
mandrillcells