2. Installation

The plugin is designed to run within ImageJ. This can be the original ImageJ (version 1) or any modified version of ImageJ such as ImageJ2 or Fiji.

2.1. Install using ImageJ2/Fiji

The SMLM plugins are distributed using an ImageJ2/Fiji update site. This allows the plugins to be easily installed and kept up-to-date. To install the plugins using Fiji just follow the instructions here:

Add the GDSC SMLM2 update site. Fiji will automatically check for a new version during start-up and install it if desired.

All the plugins will appear under the Plugins > GDSC SMLM menu.

2.2. Install using ImageJ version 1

The plugin is designed to run within ImageJ. You can obtain the latest version of ImageJ from:

To get the plugins you can download the latest Jar files from the update site and put them in your ImageJ plugins folder. The jars can be found here:

You will also need to install the additional Apache Commons Math 3 library and EJML. These are already included in Fiji so are not on the update site. You can get the files here:

Place all of the following jar files into the ImageJ plugins directory:

Jar File

Description

commons-math3

Contains math routines.

commons-rng-*

Contains random number routines.

gdsc-analytics

Contains the GDSC analytics library.

gdsc-core

Contains the GDSC core library.

gdsc-core-ij

Contains the GDSC core ImageJ library.

gdsc-smlm

Contains the GDSC SMLM library.

gdsc-smlm-ij_

Contains the GDSC SMLM ImageJ plugins.

ejml

Efficient Java Matrix Library for linear algebra. Requires version 0.24. This is the version used by Fiji.

fastutil-core

Library for type-specific Java collections.

JTransforms

Library for multi-threaded Fourier transforms.

JLargeArrays

Support library for JTransforms.

protobuf-java-*

Google protocol buffers library for readin/writing data.

mfl-core

A library for reading/writing Matlab Mat5 matrix files.

xstream

A library for reading/writing XML.

The plugins will be visible under the Plugins > GDSC SMLM menu.

An ImageJ toolset can be installed using the GDSC SMLM > Toolset > Install SMLM Toolset plugin. When selected the toolset adds a set of buttons on the ImageJ toolbar for commonly used plugins. More details can be found in section 11: Toolset Plugins.