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 |
gdsc-smlm |
Contains the GDSC SMLM library. |
gdsc-smlm-ij_ |
Contains the GDSC SMLM |
ejml |
Efficient Java Matrix Library for linear algebra. Requires version 0.24. This is the version used by |
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.