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Installation

Basic requirements

QuimP is written in Java as a set of ImageJ plugins, thus it can be run on any platform that supports Java (Windows, MacOS, Linux). A fast processor and at least 4 GB of RAM is recommended (more in case of large datasets).

The following components are required to run QuimP:

  • ImageJ (or Fiji) in version 1.43 or later.
  • QuimP core package - iinstallation through the Fiji Updater is strongly recommended.
  • Java 8 or newer runtime (provided with latest Fiji).

QuimP will best work with Fiji, an extended version of ImageJ, available here: http://pacific.mpi-cbg.de/wiki/index.php/Fiji. Fiji supports automated updating of QuimP.

Since May 2016 Fiji officially supports Java 8. Every new installation comes bundled with Java 8 and no additional effort is needed to run QuimP. For older Fiji versions (with default Java 6), one has to first install Java 8 and then switch Fiji to use external instance of Java Runtime in place of embedded one. See this link for details.

Strongly recommended: Installation procedure for Java 8 enabled Fiji through automatic update site

  1. Start Fiji
  2. Go to Help->Update Fiji then click Manage update sites.
    1. Find QuimP on the list of sites.
    2. Tick checkbox on left.
    3. Make sure that Java-8 is also ticked. It is one of the first few entries in the list.
  3. Close ImageJ updater and apply any changes proposed by Updater.

Fiji update

Possible, but not recommended: Manual installation

  1. Download QuimP in latest available version from here
  2. Copy QuimP-xxxx.jar file (xxxx string stands for current QuimP version) into plugins folder located in the installation directory of Fiji/ImageJ.
  3. Remove any other QuimP-xxxx.jar from plugins.
  4. Remove any cryptic numbers at the end of filenames (after *. jar)
  5. Run ImageJ/Fiji and head to the Plugnis menu. The QuimP-xxxx entry should be available there.

Installation procedure for old Fiji installations (with Java 6 as default)

  1. Download and install Java 8. For MacOS or Linux extra configuration steps may be necessary. Consult documentation relevant to your system.
  2. Consult Fiji FAQ how to run ImageJ or Fiji with Java 8. http://imagej.net/2016-05-10_-_ImageJ_HOWTO_-_Java_8,_Java_6,_Java_3D can be also useful.
  3. Configure Update Site.