Installation

Cell Sampler

Installation Instructions

---

• Cell Sampler
  • Installation Instructions
    • Description
    • System Requirements
    • Standard Installation
    • Source Installation
    • Adding Existing ImageJ Plugins
    • Upgrading ImageJ

---

Description

This document describes the installation procedure of the Cell Sampler plugin bundled with ImageJ.

System Requirements

• The supported platforms are Windows and Mac.
• The plugin requires a Java run-time (standard edition), version 1.6 or greater (32-bit or 64-bit).
• If building the plugin from source, you need both the Java development Kit and ANT (version 1.8.2 or greater).
• Make sure that the directories containing the Java interpreter/compiler and ANT are included in your computer's search path.
• The plugin uses ImageJ 1.46h or higher (see Upgrading ImageJ). ImageJ is supplied with the plugin.

N/B On many computers, Java is installed as standard.

Standard Installation

A standard installation means that the Cell Sampler is pre-installed with a fully configured version of ImageJ.

N/B You may wish to add existing ImageJ plugins to an installation of _Cell Sampler (see Adding Existing ImageJ Plugins)._

To do a standard installation, do the following.

1. Download the plugin ZIP file from here (size=5.5Mb).
2. Unzip the archive, a directory called cell-sampler-1.0 is created in your downloads directory.
3. Copy this directory to the desired location on your computer and rename as appropriate.
4. If using a Mac, click on ImageJ.app or ImageJ64.app to start ImageJ. When run for the first time on a Mac, a warning will appear saying ImageJ is an application downloaded from the Internet. Click Open to start the ImageJ.
5. If using Windows, click on ImageJ.exe to start ImageJ. When run for the first time on Windows, ImageJ will generate a pop-up message stating that it has configured its installation environment. Ignore that message. A file called ImageJ.cfg is created in the installation root directory; do not delete that file.

Source Installation

To build the Cell Sampler plugin and ImageJ from source, do the following.

N/B Requires both the JDK and ANT on the build machine.

1. Download the Cell Sampler source code from here (size=3.3Mb).
2. Unzip the archive, a directory called cell-sampler-1.0-src is created in your downloads directory.
3. Open a command prompt and change directory into cell-sampler-1.0-src.
4. List the contents of the current directory, you should see a file called build.xml. If you cannot then you are in the wrong directory.
5. At the command prompt type ant and press Enter. This starts ANT building the Java source code. Compilation should only take a couple of minutes, if longer then something has gone wrong with the build.
6. The application to install is placed in a directory called dist. Copy and rename this directory to complete the installation.
7. Delete the project directory (cell-sampler-1.0-src) as necessary. ImageJ is started as described in the previous section.

The compiled Java application is cross-platform, i.e. will run on either Windows or Macs.

Adding Existing ImageJ Plugins

To add exisitng ImageJ plugins to a Cell Sampler/ImageJ installation, copy the JAR/class files or directories into the plugins directory of the installation root directory of this software.
Once you have added new plugins to an installation, you will need to restart ImageJ for the change to take effect.

A list of currently available Image plugins is found here.

Upgrading ImageJ

New versions of ImageJ are released periodically.
Upgrading ImageJ means that the core software engine is replaced, but existing plugins like Cell Sampler are left unmodified.
Cell Sampler is bundled with ImageJ 1.46h.

Once you have installed ImageJ/Cell Sampler, to upgrade ImageJ, do the following.
You must be connected to the Internet for the upgrade to work.

1. Start ImageJ.
2. From the main menu go to Plugins->Tools->ImageJ Updater.
3. Once clicked, a pop-up will appear showing version numbers and asking if you wish to upgrade.
4. Click Ok if you wish to upgrade. A new version of ImageJ will download
5. Restart ImageJ for the change to take effect.
6. If you are using a Mac, you need to do the upgrade twice. Once when running ImageJ.app and once when running ImageJ64.app as both of these application possess their own copies of the ImageJ software.