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 Forum!

ImageJ Demo

First, we tell the notebook to download and install ImageJ from the remote repository.

In [1]:
%classpath config resolver scijava.public
%%classpath add mvn
net.imagej imagej 2.0.0-rc-71
net.imagej imagej-notebook 0.7.1
Added new repo: scijava.public

Now that ImageJ functionality is available to the notebook, we create an ImageJ gateway.

In [4]:
// Creates a new ImageJ2 gateway: a variable to be used as the central enrty point to any ImageJ2 functionality
ij = new net.imagej.ImageJ()
"ImageJ v${ij.getVersion()} is ready to go."
ImageJ v2.0.0-rc-71 is ready to go.

For further details, see the Fundamentals of ImageJ notebook.

Load an image

You can open images from local files as well as remote URLs.

In [3]:
image ="")

Compute histogram

In [4]:
histogram = ij.op().image().histogram(image)

N-dimensional crop

In [5]:
mandrill ="")
[INFO] Populating metadata
[INFO] Populating metadata