Introduction to Jupyter Notebooks


Why use Jupyter?

Bridge the gap between biology and code

“We used to speak two different languages. I would talk about the biology and she would talk about coding. Now we have common ground; we can communicate to each other better. This accelerates our research,”

Use your favorite languages

Run in the cloud, free, reproducible

Any notebook can be a presentation

Reveal.js is an HTML presentation framework.

The RISE extension for Jupyter makes any Jupyter notebook into a LIVE reveal.js presentation.

Like this one! 🤩

Example notebooks

  • The ImageJ Tutorial Notebooks demonstrate how to use ImageJ in a notebook with either the BeakerX Groovy kernel or with the Python 3 kernel.

Finally, an awesome walkthrough of the Python data analysis pipeline from start to finish:

In [1]:
%classpath config resolver scijava.public https://maven.scijava.org/content/groups/public
%classpath add mvn net.imagej imagej 2.0.0-rc-71
ij = new net.imagej.ImageJ()
ij.io().open("https://imagej.net/images/FluorescentCells.jpg")
Added new repo: scijava.public
[INFO] Populating metadata
[INFO] Populating metadata
Out[1]: