CrazyBiocomputing Blog

This repository contains all the JavaScript code I wrote in the blog CrazyBioComputing.

1. Digital Image
2. Processing
3. Analysis
4. 2.5D and 3D
5. Programming
6. Machine Learning

Install

Install the JavaScript source files

• In your folder ImageJ/plugins, create a sub-folder entitled crazybio
• Copy and paste the two files nashorn_polyfill.js and utils.js
• For the code contained in each section of the blog, I advise you to create a sub-sub-folder. For example, ImageJ/plugins/crazybio/ML for Machine Learning.
• For testing the sources, I suggest you to create another folder entitled MyScripts in ImageJ/plugins and create a new file with the extension .js for writing your own code.

JavaScript version

All the codes are written in a "modern" JavaScript version termed "JS2015+" or "JS ECMAScript". However, this version was partially implemented in the JDK (Java Development Kit) version 10 and 11 with a JS engine called "Nashorn". This engine was deprecated in the JDK version > 12, unfortunately...

Thus, to run these JavaScript files, you need to install and run ImageJ with a JVM (Java Virtual Machine) version 10 or 11.

1. The best option is to download the "Platform Independent" ImageJ [Link].
2. Then, go to the website OpenJDK, choose the archive versions and download version 11.
3. The last tricky part — specially if you have other JDKs in your computer — is to modify the Java path for ImageJ to be sure that it runs on the good (version 11) Java Virtual Machine.

Linux

you need to modify the file ImageJ/run. For example, if ImageJ is installed in a sub-directory bin/ in your home directory and you download the JDK in the same directory bin/. Your file run will be:

#!/bin/bash
~/bin/jdk-11/bin/java -Xmx2048m -jar ij.jar 

Windows

TODO

Mac

TODO