OMERO.insight Project

The OMERO.insight Project is a sub-project of the Open Microscopy Environment Project, OME that focuses on delivering a client for the visualization and manipulation of both image data and metadata maintained at an OMERO server site. OMERO.insight is completely written in Java. Technical documentation can be found here.

Directory Contents

This directory is the repository of the software artifacts of the OMERO.insight Project. Its contents are as follows:

+ build.gradle, settings.gradle: build for build system
+ src: Contains the application source files, various configuration
       files required by the application to run and the test code.
+ buildSrc: source files to package the applications
+ README: This file.
+ LICENSE.txt: The license covering this software.
+ CHANGELOG.md: The release history
+ FAQ.md: Commons questions

Building OMERO.insight

The compilation, testing, launch, and delivery of the application are automated by means of a Gradle build file. In order to perform a build, all you need is a JDK -- version 1.8 or later. From the command line, enter:

 gradle build

This will compile, build, test and create a distribution bundle. To run OMERO.insight from the distribution bundle unzip omero-insight.zip then go to the omero-insight directory and from the command line enter, for example:

 bin/omero-insight

To run the OMERO.importer, enter:

 bin/omero-insight containerImporter.xml

To run OMERO.insight, from the command line, enter:

 gradle run

To run OMERO.importer, from the command line, enter:

 gradle runImporter

Packaging OMERO.insight

OMERO.insight uses the Gradle java-packager-plugin and is capable of creating an installer for the platform the deployment task is run on.

Note, a Java runtime is included with the bundled installer. It is recommended to use OpenJDK as the system's JRE to avoid potential licensing issues.

In order to be able to successfully create an installer, a JDK with javapackager or an OpenJFX SDK matching the version of the system JDK is required (particularly if you intend to build with JDK 11 or higher).

OSX

If you are using Homebrew, you can install, for example, OpenJDK 8 which comes bundled with JavaFX. To install run:

  brew tap bell-sw/liberica
  brew install --cask liberica-jdk8-full

Windows

Scoop:

  scoop bucket add java

  scoop install zulufx8

Manually:

To set up a build environment with Windows without using a package manager such as Scoop or Chocolatey perform the following:

JDK:

1. Download ojdkbuild.
2. Run the installer.
3. Once at the custom setup page of the setup select the OpenJDK Runtime drop-down and install the JAVA_HOME feature.
4. Whilst on the custom setup page, select to include the OpenJFX Runtime.

Inno Setup (required to create .exe installer):

1. Download and install Inno Setup.
2. Add the Inno Setup install directory (e.g. C:\Program Files (x86)\Inno Setup 5) to the PATH.

You can install Inno Setup using Chocolatey:

  choco install innosetup

Depending on the Windows version you are using, you might not be able to use the latest version of Inno Setup.

WiX (required to build .msi installer):

1. Download and install WiX 3.0 or greater.
2. Add WiX to the PATH.

Packaging

To run the application packager, from the command line enter:

Windows

 gradle packageApplicationExe

OSX

 gradle packageApplicationDmg

Developing OMERO.insight

See https://docs.openmicroscopy.org/latest/omero/developers/index.html#insight.

OMERO.insight extension

1. To use the metadata extension OMERO.mde, set the following entry in container.xml or in containerImporter.xml to true:

<entry name="omero.client.import.mde.enabled" type="boolean">false</entry>

FAQ

See FAQ.md

Licensing

This software is licensed under the terms of the GNU General Public License (GPL), the full text of which can be found in the top level LICENSE.txt. See https://www.openmicroscopy.org/licensing/ for further details.

Copyright

Copyright (C) 2006-2022 University of Dundee. All rights reserved.