PART 1: INTRODUCTION TO FIJI INTERMEDIATE

Requirements for undertaking FIJI Intermediate

This workshop assumes that you are familiar with the basic features of FIJI/ImageJ and now want to apply those functions to multi-dimmensional images and image analysis

Analysis Tools in FIJI

FIJI is an open-source software, which means everyone can use it but also means everyone can add features and expand FIJI’s capabilities. Researchers who developed a specific image analysis pipeline for their project and want to make it available to other researchers can add it to FIJI as a so-called plugin. For this reason there are a wide range of analysis tools available in FIJI, and in some cases multiple tools which have the same outcome.

These workshops are not able to cover every tool availble in FIJI, but here we will be focusing on the most common types of image analysis and where possible will demonstrate different methods available. For some analysis tools which have multiple plugins we may feel that one is more accurate or approporiate than the other, and in these circumstances we will only focus on the more suitable analysis tool.

Plugins Required From Separate Downloads

Some plugins are pre-installed in FIJI, others you will have to download and install yourself. We will be using both types of plugins in this workshop. The following plugins will need to be downloaded and installed.

Drift Correction/Image Registration: Google ‘StackReg FIJI’ and ‘TurboReg FIJI’ and download both plugins. They will appear as zipfiles. Unzip both files and then move the .jar file into the plugins folder of your FIJI software.

Deconvolution: Download Iterative_Deconvolve_3D.class from http://imagej.net/Iterative_Deconvolve_3D

Note: There’s also an Iterative_Deconvolve_3D.java available. The.java file does not work and you need to make sure you download the .class file instead.