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1. Installation

There is also a Listing of All Programs that gives a one-line description of each IMOD program and a link to its man page.

1. Installation

All of the IMOD programs are available via the IMOD Download Page. The distribution is bundled together using the tar program with gzip compression, then placed in a file after a shell script that can extract and install the programs. For Windows and Mac, there is an executable installer than runs this script; for Linux you need to run the script yourself at the command line. If you are willing to install to the default location in the system and set up the IMOD environment for all users in the default way, then you can use the installers on Windows and Mac, and install on Linux simply by running the script, e.g.,
sh imod_4.11.1_RHEL6.sh
(In this guide, the specific filenames with '4.11.1' are used as an example; you should always substitute the full name of the file that you are installing for the one shown here.) You cannot click on the .sh file to install it. This command will not work on Windows unless the Cygwin toolkit is installed. The executable installer for Windows (with extension .exe) does work by clicking on it to install (either with or without Cygwin). If you have followed our recommended installation procedures in the past, you will be able to upgrade using the same method. If you want to install to a location other than the default, you can specify the desired location inside of which the IMOD directory will be placed, e.g.,
sh imod_4.11.1_RHEL6.sh -dir /opt
Older versions will be renamed, and at the end the installation script will offer to remove them for you.

After installing for the first time, you will probably need to start a new terminal window to be able to run IMOD programs; on Ubuntu you will probably need to log out and log back in.

People with special requirements not anticipated by the install script may need to work with the tar file instead. It can be extracted with:
sh imod_4.11.1_RHEL6.sh -extract

The gzipped tar file and the install script will be left in a subdirectory named IMODtempDir. There are several other useful options: -script to install startup scripts to a different location, -skip to skip installing startup scripts, -name to have the IMOD directory be renamed to the given name. Use:
sh imod_4.11.1_RHEL6.sh -help
to see all available options. The sections below on individual machine types describe what will be done by the default installation procedure. They also list the steps for doing a manual installation instead of using the self-installing package, but this should rarely be needed.

1.1. Installing Java for Etomo.

To run Etomo, you need a Java run-time environment (JRE), version 1.7 or higher, installed and accessible to IMOD. You should use an OpenJDK version of Java. Most Linux distributions have an OpenJDK package available if not in the default install. On Ubuntu 18 and 20, OpenJDK java can be installed with
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sudo apt install default-jre
For Red Hat 8, the default install includes only a 'headless' version and you will need to install a proper version with
sudo yum install java-1.8.0-openjdk
where you could use java-11-openjdk instead.
For Windows, Mac, and other Linux distributions, you will need to download a package. A good source of installer packages is AdoptOpenJDK. Oracle now requires a paid license for most Java packages and you are probably not eligible to run one of their installer packages for free. (You can use one for free if your institution has a license or you are not being paid to work with IMOD.) Their 'open source' packages are free but currently are not installers, just compressed archives that do not make the program easily runnable. On a Mac, this means that when you try to run Etomo with no Java installed, if the OS puts up a message that takes you to the Oracle site, you should ignore it.

Download a JRE from the AdoptOpenJDK releases page. If you start at the AdoptOpenJDK home page, press the 'Other platforms' button to get to this page; the 'Latest Release' button on the home page downloads a Java software development kit (JDK) that is considerably larger and is not needed. You can choose the latest release or one of the releases marked as LTS (long term support); they are all compatible with Etomo and all are being maintained with security updates. Keep the default selection of the JVM, the HotSpot. Download a JRE for your operating system.

Windows. Click on the installer to run it and take the default options, in particular the one to put Java on the path.

Mac OS. Click on the installer to run it. It will install to /Library/Java/JavaVirtualMachines. By some mysterious means, running /usr/bin/java should end up running the highest version in this directory (or the most recent installation, if there is both a JRE and a JDK of that version). To verify that it is running the intended version, enter
java -version
In IMOD 4.11, the Etomo startup script in these packages will look for the latest directory in /Library/Java/JavaVirtualMachines and run the Java there. If this fails or is not running the right version, there are two options:

Set the environment variable IMOD_JAVADIR to the directory in the package containing the bin directory, for example
export IMOD_JAVADIR=/Library/Java/JavaVirtualMachines/adoptopenjdk-12.jre/Contents/Home
To set this on a system-wide basis, you can make a file IMOD.sh in /usr/local/ImodCalib with this line; or you can add the line to /etc/profile and /etc/zprofile in the place where the IMOD environment is set.
Put the bin directory in the package on your path, for example
export PATH='/Library/Java/JavaVirtualMachines/adoptopenjdk-12.jre/Contents/Home/bin:$PATH'
To do this on a system-wide basis, make either of the two changes described for option 2.

Linux. If your distribution does not provide OpenJDK packages, see if you can use the RPM or DEB install packages from AdoptOpenJDK and follow the instructions there for installation. Otherwise, you will need to get one of their .tar.gz packages and untar in a location of your choice. Then you have two options: set the environment variable IMOD_JAVADIR to the top Java directory; or add the bin directory that it contains to your PATH. Act act driver. To do either of these on a system-wide basis, you can put the appropriate line in files IMOD.sh and/or IMOD.csh in /usr/local/ImodCalib.

Java is notoriously insecure when run in browsers and requires frequent updating if a browser is enabled to run Java. The frequency of security vulnerabilities when using it just to run a program like Etomo is less clear; but it is a good idea to keep it up to date.

1.2. Setting Up a Linux PC to Run IMOD.

IMOD development for Linux is done on Red Hat Workstation 7 with NVIDIA cards, and computation on the graphics card is supported only for NVIDIA cards. For graphics (e.g., IMOD model display), AMD cards are a reasonable alternative. We actively maintain compatibility with Ubuntu, and deal with issues that come up on other Linux distributions as necessary.

NVIDIA installation. Installing NVIDIA drivers is straightforward on some systems, but here are some instructions that may be helpful for older Fedora and for Red Hat/Centos through version 7. The latest ve