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.
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.
sudo apt install default-jre sudo yum install java-1.8.0-openjdkDownload a JRE or JDK from the Adoptium releases page. If you start at the Adoptium 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, or a JDK if a JRE is not available.
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:
bin directory, for example export
IMOD_JAVADIR=/Library/Java/JavaVirtualMachines/adoptopenjdk-12.jre/Contents/Home
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.bin directory in the package on your path, for example export
PATH="/Library/Java/JavaVirtualMachines/adoptopenjdk-12.jre/Contents/Home/bin:$PATH"
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. 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.
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 versions of the drivers change the Driver line in
/etc/X11/xorg.conf from "nv" to "nvidia" if you accept their offer to modify
the file. For recent Fedora, search for "Install NVIDIA drivers
Fedora xx", where xx is your version number, and study the
various instructions that you find.
On Ubuntu, the automatic installation through Synaptic Package
Manager or its current equivalent should be adequate. However, on
laptops, it is important to know whether the NVIDIA card has Optimus
technology for switching between the card and built-in graphics. If it
does, the regular methods will probably not work, but one solution is to
install bumblebee (search on bumblebee and the Linux distribution name
for specific instructions). Bumblebee allows you to control which
graphics device programs use. At least as of a few years ago, you could
direct a program to access the NVIDIA graphics by starting it with a
the optirun command. Thus, if you simply start a new
shell, e.g., with optirun bash and run IMOD commands from
this shell, you should find that 3dmod uses the NVIDIA graphics and that
the GPU is available for reconstruction.
Java for Etomo.
To check whether you have Java installed, run the command
java -version
If there is no Java or it is not an OpenJDK version, see
1.1 Installing Java for Etomo..
Python on Ubuntu 18 and 20 and Red Hat 8.
Ubuntu 18 and 20 and Red Hat 8 install with Python 3 and not 2, and this Python runs
with the command python3. IMOD scripts run fine with
Python 2 or 3, but rely on a program named python being on
the search path. The IMOD installer will offer to make a link from
/usr/bin/python3 to /usr/bin/python, or you
can use the Python 3 just for the IMOD install, then install Python 2
explicitly if you want to use that for some reason. On Ubuntu you can
do so with
sudo apt install python
and if the IMOD installer made a link in /usr/bin, it will be replaced
when you install Python 2. On Red Hat 8, you can install Python 2
with
sudo yum install python2
but the executable is named python2, and if the IMOD
installer made a link
in /usr/bin, it will be removed. You will need to make a
link yourself, with
sudo ln -s /usr/bin/python2 /usr/bin/python
tcsh for Ubuntu, Fedora, or Red Hat 8.
Only a few very specialized scripts in IMOD require tcsh,
although you would need it to install very old versions of IMOD with
package names ending in .csh instead of <.sh.
The standard Red Hat 8, Fedora, and Ubuntu installs do not include it. If you find
that you need it, you can install it on Ubuntu with:
sudo apt-get install tcsh
or on Fedora or Red Hat 8 with:
sudo yum install tcsh
The self-installing package will install to a directory named IMOD
under /usr/local unless given an alternate location to /usr/local
with the -dir option. It will copy the startup scripts IMOD-linux.sh
and IMOD-linux.csh to /etc/profile.d. unless
given an alternate location with the -script option or told to
skip this step with the -skip option, or unless you are running
an Ubuntu version before 10 or give the -debian
option. It the latter cases, it will
modify /etc/bash.bashrc and /etc/csh.cshrc to
source the startup scripts from the IMOD directory, unless you give the -skip
option. To accomplish all of this, change directory to the place where
the package is located and enter, for example:
sudo sh imod_4.11.1_RHEL7-64_CUDA8.0.sh
You will have to open a new window, or possibly even log out and log back in,
for the installation to take effect.
If you are upgrading IMOD using the default procedures, and your previous
installation used another method for setting the environment variables for
users, be sure to remove whatever commands were used before. These might
have been placed in /etc/profile, /etc/cshrc,
/usr/local/etc/cshrc,
or users' .bashrc, .bash_profile, or .cshrc
files.
You would skip the installation of the startup scripts if you do not want a
system wide installation, or if you are installing to a server to be accessed
by multiple workstations. In this case, you would place the following in
the .bashrc or .bash_profile
of individual users running the bash shell (where
<location of IMOD> is the absolute path to the IMOD directory):
export IMOD_DIR=<location of IMOD>
if [ -e $IMOD_DIR/IMOD-linux.sh ] ; then source $IMOD_DIR/IMOD-linux.sh ; fi
or, place the following in the .cshrc
files of individual users of tcsh :
setenv IMOD_DIR <location of IMOD>
if (-e $IMOD_DIR/IMOD-linux.csh) source $IMOD_DIR/IMOD-linux.csh
Alternatively, if there are system-wide startup scripts sourced from
the users' .bashrc/.bash_profile or .cshrc, you
would place these commands in the system-wide startup scripts. You
should always source the startup script that comes with an IMOD
distribution, not make a copy of the startup script and incorporate it
into other scripts, because that is the easiest way to adapt to changes in
the startup script between versions.
If you want to run programs temporarily in a particular version of IMOD without
replacing your installed version, unpack the desired version in some logical
place with a command like:
sh imod_4.11.1_RHEL7-64_CUDA8.0 -dir
testIMOD -skip
This will manage an installation of IMOD under the directory testIMOD,
offering to delete other versions there. To run with this IMOD, cd to testIMOD/IMOD
and enter:
export IMOD_DIR=`pwd` (under bash,
or) setenv IMOD_DIR `pwd`
(under tcsh)
source IMOD-linux.sh (under bash,
or) source
IMOD-linux.csh (under tcsh)
Manual Install. To install manually from the tar file, do the
following steps after running the self-installing file with the -extract
option:
mv imod_4.11.1_RHEL6.tar.gz /usr/local
cd /usr/local
tar -xzf imod_4.11.1_RHEL6.tar.gz
ls -l
IMOD
-> imod_4.7.15), then enter
rm IMOD
mv IMOD oldIMOD
ln -s imod_4.11.1 IMOD
cp IMOD/IMOD-linux.* /etc/profile.d On early Ubuntu or Debian systems, when installing manually, instead of
step 8, you would insert commands into /etc/bash.bashrc
and /etc/csh.cshrc just like
those given above for inserting in users' .bash_profile and
.cshr files, respectively.
Rosetta2 for M1 Macs. To install IMOD 4.11 on an M1-based Mac, Rosetta2 must be installed. IMOD 4.11 currently runs only through this emulator, but a package compiled for M1 is available in IMOD 4.12 beta.
Python for OS 12. The default installation in OS 12.3 no longer includes Python. You must install a Python first to install IMOD. The recommended option is a package from python.org; here is a Python 3.9.11 universal installer package that runs on Intel and M1 processors. Installed, this package takes about 180 MB if documentation is omitted. Another option is to install Python through homebrew. The third option is to install the Apple Developer Command Line Tools, which the system will offer to install if you enter "python3" at the command line. This package takes 2.2 GB. The IMOD installer will recognize all of these Pythons regardless of whether they are on the search path, and if you install some other Python, it needs to be on the search path and you will probably need to use the command-line self-installing package instead of the clickable installer.
Installing IMOD
The clickable installer (ending in ".pkg") will install to /Applications
and will place appropriate source commands in /etc/profile,
/etc/zprofile, and /etc/csh.login. You will
need administrative privileges to use this installer.
After installing on OS 11 or 12, the Launchpad (multiple icon display) will show IMOD with two tempting icons inside, 3dmod and Qt Assistant. It will not work to click on 3dmod or Qt Assistant.
The package built under OS 10.14 is fully signed and the system should not object when you try to install it in OS 10.14, 10.15 or 11.0. If for some reason you need to install a package built on an earlier OS, there are two options. You can click on the question mark in the upper right of the message that you get when you try to run the package; it will direct you to open the Settings - Security and Privacy - Private tab where you can confirm the installation after dismissing the installer message. Or, you can use the command-line package described next.
The command-line self-installing package (ending in ".sh") will install
to /Applications or to an
alternate location with the -dir option.
The ".sh" file will
not work by clicking on it, only by running it at the command
line. It will place appropriate "source" commands for defining the user
environment in /etc/profile, /etc/profile, and
/etc/csh.login. You need to be able to use sudo. Open a
terminal window (under Applications-Utilities), change directory to the place
where the package is located, and enter, e.g.:
sudo sh imod_4.11.1_osx10.11_CUDA8.0.sh
You will need to exit and restart Terminal for changes from the
installation to take
effect, or you can just source /etc/profile (if you are
running bash), /etc/zprofile (if you are running zsh) or
/etc/csh.login (if you are running tcsh). If
you are upgrading IMOD with the default installation procedures and your
previous installation used another method of setting environment variables,
then you may need to remove "source" or other environment-setting commands from
various files, such as /etc/profile, /etc/csh.login,
or users' .bashrc, .profile,
or .cshrc files.
Fixing an IMOD Installation after a System Update. On OS 11 or 12,
system updates may replace the files in /etc that source the
IMOD environment-setting commands, and IMOD will stop working. To
recover from this without reinstalling IMOD, run the command
sudo /Applications/IMOD/fixMacInstall
or if IMOD is installed elsewhere, run
sudo pathToIMOD/fixMacInstall
where pathToIMOD is the full path to the IMOD directory.
If this command fails with "Command not found", it is probably because
there is no Python runnable as "python" on the path, in which case this
should work:
sudo /Applications/IMOD/pythonLink/python
/Applications/IMOD/fixMacInstall
Setting Up Ability to Click on Files or Drag
and Drop onto an Icon to Open them in 3dmod.
Once you have verified that IMOD programs run from the terminal after
installing them, you can associate
files having desired extensions
(e.g., .mrc or .rec) with a script that will open
files in 3dmod. The steps are:
You can also drag and drop a file onto openIn3dmod to open it. Open a Finder and find /Applications/IMOD/bin/openIn3dmod. Drag this to the dock if you want it there.
If you install IMOD in a location other
than /Applications, you will need to be able to get to it in
the file association chooser, or you will need to copy
the openIn3dmod.app directory to another location that you
can get to.
In general, you cannot run 3dmod by clicking on its icon ("3D") in
/Applications/bin/IMOD. However, this is possible
if you have installed an unsigned package built under an older OS
(i.e., 10.11). In that case you can also
make some links in /usr/local/lib to libraries in the IMOD directories
that will allow you to start 3dmod by clicking on its
icon. (This is not needed
for the file association and drag-and-drop to work and does not work
with a signed package.) Run the linklibs-mac
script by entering:
sudo $IMOD_DIR/linklibs-mac -i $IMOD_DIR
If this creates problems, such as conflicts with other programs that supply
their own Qt libraries, you can remove the links with:
sudo $IMOD_DIR/linklibs-mac -u $IMOD_DIR
If you are upgrading IMOD and have done this before, you should
run sudo $IMOD_DIR/linklibs-mac
-u $IMOD_DIR before installing the new version then rerun with
the -i option after installing.
Once the links are made, test that 3dmod will start by finding it in
the IMOD/bin and clicking on it.
Installing Java.
To check whether you have Java installed, you can try to
start Etomo by entering etomo, or just enter java
-version in a terminal. If it is not installed, you will get a
message from the operating system offering to take you to the
Oracle site. Ignore this message and see
1.1 Installing Java for Etomo..
Using a 3-button Mouse. The
one-button mouse on the Mac can be used in 3dmod with some
keyboard modifiers, but this is painful. Just get a 3-button mouse.
It may just work when you plug it in, so try it in 3dmod
before installing drivers. Installing Logitech and some other drivers may
actually make it stop working, and the solution is to uninstall the drivers.
Manual Install. To install manually from the tar file that you can
get by running the self-installing file with the -extract option,
you have two alternatives. To do it from the command line, open a Terminal
window and:
sudo mv imod_4.11.1_osx_intel64.tar.gz /Applications
cd /Applications
sudo tar xzf imod_4.11.1_osx_intel64.tar.gz
ls -l
IMOD
-> imod_3.1.6), then enter
sudo rm IMOD
sudo mv IMOD oldIMOD
sudo mv imod_4.11.1 IMOD
You also need to add some startup commands to the system
files /etc/profile and /etc/csh.login , unless they
are already there from a previous installation of IMOD. Use sudo to invoke
emacs or pico on these files, .e.g.:
sudo emacs /etc/csh.login
Copy the text in IMOD/mac.profile to the end
of both /etc/profile and /etc/zprofile, specifically the command
[ -r /Applications/IMOD/IMOD-mac.sh ] && source
/Applications/IMOD/IMOD-mac.sh
Similarly, copy the text in IMOD/mac.cshrc to the end of /etc/csh.login,
specifically the command
if (-e /Applications/IMOD/IMOD-mac.csh) source
/Applications/IMOD/IMOD-mac.csh
If you want to install at another location, change /Applications/IMOD to
the name of the top IMOD directory in IMOD-mac.sh and
IMOD-mac.csh and in the
source commands placed in /etc/profile and /etc/csh.login.
If you are sure you are not going to install somewhere else in the future, you
can avoid modifying IMOD-mac.sh and IMOD-mac.csh by
defining IMOD_DIR before the source commands, i.e. with
export IMOD_DIR=<Location_of_IMOD>
before the source command in /etc/profile, or with
setenv IMOD_DIR <Location_of_IMOD>
before the source command in /etc/csh.login.
See the above instructions for Linux PC for other variations on installation procedures.
To use IMOD effectively under Windows,
you need to install either a Unix-like
environment called Cygwin or an
appropriate version of Python. In the latter case,
everything in IMOD will work except a few
specialized C-shell scripts, but subtomogram averaging with PEET will
not work without Cygwin. If this is the route that you prefer, go
to Setting Up a Windows PC and Installing
IMOD without Cygwin. A third, less useful way of running IMOD on a
Windows PC is described in Using IMOD
under "Bash on Ubuntu on Windows". In any case, you will need
Java installed to run Etomo. ou See 1.1 Installing Java for
Etomo both for instructions and for information on license restrictions
with Oracle Java. To check whether you have Java installed,
you can try to start Etomo by entering etomo, or just
enter java -version in a terminal or Command Prompt window.
This section deals with installing Cygwin. We have provided both a Cygwin package and a Cygwin installer to make the installation process simpler and more predictable. Use the installer when installing for the first time. This installation will occupy ~220 MB for the 32-bit version, or ~500 MB for the 64-bit version, all located under a single directory that can be removed easily. The installation will also create icons on the desktop and in the Start Menu, and make several simple entries to the Windows registry. To satisfy the terms of the Cygwin open source license, we also provide the source code matching the binaries in our package. The download links are in the table; the package from October 2014 must be used on Windows XP; the packages from January 2017 or December 2020 must be used on Windows 10. If you plan to upgrade or add to your installation, get the 64-bit one because only 64-bit is now supported.
| Date | Runs on | ||||
| December 2020 | Windows 10 | 64-bit | Cygwin Installer | Cygwin Package | Matching Source |
| January 2017 | Windows Vista -> 10 | 32-bit | Cygwin Installer | Cygwin Package | Matching Source |
| October 2014 | Windows XP -> 8 | 32-bit | Cygwin Installer | Cygwin Package | Matching Source |
Installing Cygwin creates a Unix-like directory tree (including directories bin,
etc, usr, and home) under its top
directory, which is C:\cygwin by default. Terminal windows
and Cygwin programs such as the Unix tools will display and work with Unix-type
paths that are relative to the top Cygwin directory. For example, if you
install Cygwin in C:\cygwin, then the location where IMOD will be
installed is referred to as /usr/local/IMOD from within Cygwin and
will exist in the Windows file systems as C:\cygwin\usr\local\IMOD.
The Cygwin that you use must include Python, which is
required for building tomograms. It is included in our packages.
If you use a current version of Cygwin from the Cygwin
website, you may need to make sure that there is a Python executable, /bin/python.exe,
recognizable to Windows (see below).
Our Cygwin packages also include a superior terminal window called mintty,
a lightweight text editor, nano,
and the vi editor.
The primary advantage of the
mintty window is that you can copy and paste just like under Unix
(highlight with left mouse button, paste with middle mouse button). This
capability uses the Windows clipboard, so you can copy text in a Windows
program (Ctrl-C) and paste with the mouse in the mintty window, or
highlight in the mintty window and paste in a Windows program with
Ctrl-V. Another advantage is that you can resize the mintty window
horizontally as well as vertically.
Cygwin installation will work best if you are logged in as a user with Administrative privileges.
Use our Cygwin installer for a fresh installation of Cygwin. It performs all the steps described below. Simply click on it; it will unpack itself and launch the Cygwin setup program as well as show a page with some instructions. Note the following points:
cygwin
as the directory name.
mintty
window running either a bash or a tcsh
shell.
.minttyrc there that
will give good starting properties for a mintty
window.
.minttyrc will also be left in
/usr/local for other users to copy.
Sometimes there are permission problems that might prevent the installer
from copying some files at the end of the installation, or that result
in errors or prevent the creation of some files during tomogram setup in
Etomo. If this happens, try editing the file /etc/fstab
within Cygwin with one of the provided editors. This line
determines how all drives should be mounted (including permissions):
'none /cygdrive cygdrive binary,posix=0,user 0 0'
'none /cygdrive cygdrive binary,noacl,posix=0,user 0 0
In order to run Etomo, you also need to have Java installed. Again, see 1.1 Installing Java for Etomo.
You can use our simpler Cygwin package instead to install Cygwin, but then you would have to do all the steps described below yourself. You can also use this package to upgrade a previous Cygwin installation. The rest of this section has steps for installing or upgrading Cygwin from this package:
setup.exe program and a CygwinMaster
folder with all the packages.
setup.exe
C:\cygwin unless you want it on a different
disk. Do not install under a directory with spaces in its name. In
the rest of this document, C:\ is used in the examples, and you need to
substitute your location if it is different.CygwinMaster
folder as the Local Package Directory
After installation you will get an icon that will start up a shell under
bash. The first time that you run this, a home
directory is created in /home
(C:\cygwin\home) and some bash startup
files are copied there.
The CygwinMaster folder contains two shortcuts and a configuration
file that make it easy to use mintty. To use mintty:
Cygwin-bash.lnk or Cygwin-tcsh.lnk from
CygwinMaster
to your desktop, depending on your preferred shell.
minttyrc from CygwinMaster
to your Cygwin home directory.
minttyrc to .minttyrc with
the command mv minttyrc .minttyrc
(you cannot do this in Windows Explorer).
mintty window.
You can right-click in the title bar of the window and select Options
to get a dialog for adjusting font size and style, colors, default window size,
etc..
Cygwin-bash
or Cygwin-tcsh shortcut to Cygwin.
minttyrc
from the CygwinMaster folder to some other place where the users
can access them (such as /usr/local).
Occasionally you will get an annoying warning in a terminal window starting with cygwin warning: MS-DOS style path detected. To eliminate this, you need to define an environment variable in Windows with the name CYGWIN and the value "nodosfilewarning". To do so, right click Computer or My Computer on the Desktop, browser window or Start menu, select Properties, Advanced or Advanced System Properties, then press Environment Variables. Press "New" in the "User variables" or "System variables" section. Enter "CYGWIN" as the name and "nodosfilewarning" as the value (without the quotes).
If you want to customize your Cygwin installation instead of using our package,
go to www.cygwin.com, click on "Setup", and
follow the installation procedures. In addition to the
default installation, it is essential that you select
python from the
Python category. In addition, there must be a Python executable named
/bin/python.exe, not
just a Cygwin link to an executable. The IMOD installer will take care
of creating such an executable, but if you upgrade Cygwin without re-installing
IMOD, you should do the following:
fixCygPython.sh.
/usr/local/IMOD/fixCygPython.sh.
ls /bin/python*
python.exe
python2.7.exe (or whatever numbered
executable shows up in the listing) withln -f /bin/python2.7.exe /bin/python.exeFor Windows, we provide an executable installer that works by clicking on it,
installs IMOD in /usr/local, copies the startup scripts IMOD-cygwin.sh
and IMOD-cygwin.csh to /etc/profile.d, and takes care
of putting Cygwin on the system path and setting the environment variables IMOD_DIR
and HOME as described below. Old versions of IMOD are
automatically deleted. If you need something besides this behavior, you
can still run a self-installing package (e.g., a sh file like imod_4.11.1_win32.sh)
at the command line, as described below.
To use the installer, just click on it. If you get a message from Defender SmartScreen that "Windows protected your PC", press More info instead of Don't run, then press Run anyway. If you then get a message from User Account Control asking if you want this app to make changes to your device, press Yes. When the installer finally starts, press buttons to confirm each step. There are no choices to make. Open a new Cygwin window and you should be able to run IMOD programs.
Here are some optional steps, whichever way you install IMOD:
bin directory (e.g., C:\cygwin\usr\local\IMOD\bin)
to the Windows path, in which case you will be able to run everything,
including shell scripts, from a DOS window.
C:\Users, following the procedure described below in
the paragraph To define an environment variable in Windows.
nda, mtk, mtoverlap), you can install
ghostscript and
gsview for Windows.
The rest of this section describes other ways of installing IMOD. If you run a
self-installing package at the command line instead (with filename ending in .sh),
it will install IMOD in /usr/local and copy IMOD-cygwin.sh and IMOD-cygwin.csh
to /etc/profile.d, unless given options telling it to do something
else.
It will not work by
clicking on it, only
by executing it from the command line. To install or upgrade IMOD this way,
start a Cygwin terminal window, change to the directory where the package is
located, and enter, e.g.:
sh imod_4.11.1_win.sh
You will have to open a new Cygwin window for a new installation to take effect.
After installation at the command line, everything can be run from a
Cygwin window. In order to run from a Command Prompt window or
to run Etomo by clicking on a shortcut to etomo.cmd, you
also need to define some environment variables inside Windows:
rundll32 sysdm.cpl,EditEnvironmentVariables
IMOD_DIR to be C:\cygwin\usr\local\IMOD
HOME to be C:\cygwin\home\username
PATH, press "Edit", and add C:\cygwin\bin;
to the front of the path (the ";" is a separator).
Even if you are not running Etomo, if you installed to a drive other than C:,
you should define IMOD_DIR as an environment variable in
Windows as described above, but with the appropriate letter instead of C, so
that 3dmod will be able to find help files if it is started by
clicking on an icon.
The steps for manually installing from the tar file instead are:
/usr/local either from
the command line or from an Explorer window, where the location will appear as
C:\cygwin\usr\local.
/usr/local and, if you have an existing IMOD
installed, rename it. cd /usr/local
mv IMOD oldIMOD tar -xzf imod_4.11.1.tar.gz
mv imod_4.11.1 IMOD
cp IMOD/IMOD-cygwin.* /etc/profile.dTo install IMOD without Cygwin using our installer package, you need to have Administrator privileges on Windows versions past XP because, for now, the installation can go only in C:\Program Files.
You must have Python installed to use IMOD fully on Windows, as well as a module called psutil built for the same version of Python. The IMOD installer relies on the registry entries made by Windows Python packages from the Python download site to find Python, so a package from there is probably needed to use the installer. There is no need to upgrade if you already have a Python installed that works for IMOD; for the purposes of running IMOD, there is no benefit to having a newer Python. Some packages are provided here:
Unless you know or anticipate that other software will need Python 2.7, you might as well install Python 3. If you need to use a Python package other than the ones here, get a matching version of psutil from the psutil site; use the Download link to get to the various versions.
For older Python, click on the downloaded Python file to install it; it installs without
using "Run as Administrator". For Python 3.8, right click on the file and
select "Run as Administrator". Python does not need to install in the
default location that it offers;
you can put it in C:\Program Files under the name of the version (e.g.,
set the install location to C:\Program Files\Python3.3).
Check the option to add Python to the PATH if one is present, and you
might as well let it disable the path length limit if that is
offered. If you
customize the installation to leave out unneeded components (e.g.,
Documentation, tcl/tk, and the test suite), be sure to keep PIP if that
is listed.
Next install psutil. For older version such as those for Python 2.7
and 3.3 in the links above, right click on the file and select
"Run as Administrator". Newer versions, like the one for Python 3.8
above, come in a ".whl" file that installs with the Python package
installer pip. Open a
Command Prompt window as Administrator by right clicking on its icon and
selecting "Run as Administrator". (One way to run it is to open the Start
menu and type "cmd"; Windows should offer Command Prompt as the best match
and you can right-click on that.) Then cd to the
location of the psutil file (e.g., cd
C:\Users\username\Downloads where "username" is your account name).
Finally enter, for example,
pip install psutil-5.7.3-cp38-cp38-win_amd64.whl
(You can type the Tab key after "psutil" and it will complete the
name.) You can ignore the warning that a newer version of pip is
available unless you plan to install more packages.
After Python and psutil are installed, click on the IMOD
installer. If you get a message from Defender SmartScreen that
"Windows protected your PC", press More info instead of Don't
run, then press Run anyway. If you then get a message
from User Account Control asking if you want this app to make changes to
your device, press Yes.
When the installer finally starts, press buttons to confirm each step;
there are no options. It will
install IMOD in C:\Program Files\IMOD, define the environment
variables IMOD_DIR, IMOD_PLUGIN_DIR, and
HOME, and place both IMOD and the version of
Python that it finds on the path. For Windows Vista and higher, it will
also define IMOD_CALIB_DIR to
be C:\ProgramData\IMOD.
In order to run Etomo, you also need to have Java installed. Again, see 1.1 Installing Java for Etomo.
If you want to use a better terminal window than the Command Prompt
window, try getting the Console program from
sourceforge. This
program allows window resizing, font and color control, easy cutting and
pasting with mouse buttons, and multiple tabs.
Unzip the package wherever you want to; it will create a directory
"Console2" with Console.exe inside, to which you can create a shortcut on your
desktop. This
configuration file has some good initial settings. Make a folder
named Console inside
C:\Users\yourUserName\AppData\Roaming (on Window 10) or
C:\Users\yourUserName\Application Data (on Windows 7)
and place the file in that folder.
There is no man command for viewing program manual pages,
but imodhelp programName will open Qt Assistant to the
manual page for the given program. The program name can even be
abbreviated.
If there will be multiple IMOD users of the system, they should add HOME
environment variables to point to their directories in C:\Users.
Without Cygwin, environment variables can be set only through a
Windows dialog that can be opened by various means, all described in the
section above, To define an environment variable
in Windows. There is no IMOD startup script, so ignore any
references to IMOD startup scripts below.
If you want to upgrade to a beta version after you have installed IMOD
from one of the executable installer packages, you should find and use an
executable installer on the beta download site. If not, or to install a
nightly build, you need to download the appropriate self-installing
package file, for example, imod_4.12.12_win64_NoCUDA.sh. Copy the
file installIMOD from C:\Program Files\IMOD to
the same place that you put the package, which should NOT
be C:\Program Files\IMOD. Open a Command Prompt window by
right-clicking on a shortcut and
selecting "Run as Administrator". In the terminal, cd to
the folder with the files and enter (for this example file)
python installIMOD -skip imod_4.12.12_win64_NoCUDA.sh
IMOD can be run under the "Bash on Ubuntu on Windows" environment in Windows 10, but this has several disadvantages. The many programs that use OpenMP to access multiple cores will only be able to use one core, and there is no access to hardware acceleration of model displays or to the GPU for computing. This environment is a way to run Ubuntu on a Windows PC, not a way to have Linux tools in the Windows environment. The Ubuntu installation is larger than Cygwin (~1100 MB), and to some extent, it would have to be maintained as a separate operating system. Although the Windows filesystem can be accessed, Windows programs, including the IMOD distributions for Windows, cannot be run. Nevertheless, if you wish to use IMOD under this environment, here are the things to know:
sudo apt-get install default-jre
xming.
sudo apt-get install Xorgexport KMP_AFFINITY=disabledexport DISPLAY=:0
Parallel processing is done in IMOD by dividing a job into multiple
parts and using Processchunks
to execute the chunks on multiple processors. Almost all parallel
processing is done through Etomo, which uses Processchunks.
The processors can be either all on one machine,
on multiple machines, or on a cluster queue. (See the
Queuechunk man page for the
definitive list of supported cluster types.) Multiple
machines or a cluster need to be defined in a
file cpu.adoc that is located in the directory
pointed to by the environment variable IMOD_CALIB_DIR (default
/usr/local/ImodCalib, or C:\ProgramData\IMOD
on Windows without Cygwin). See the example cpu.adoc file
in $IMOD_DIR/autodoc and
the manual page for cpu.adoc for full
details on configuring this file.
For a single machine with multiple CPUs, there are three simple options for enabling the parallel processing through Etomo:
[Computer = localhost]
number = 4export IMOD_PROCESSORS=4 (for bash users)
setenv IMOD_PROCESSORS 4 (for tcsh users)
We recommend using only the number of physical cores on the system
when there is hyperthreading available. For the computational tasks in
IMOD, using more than the number of physical cores is usually of little
benefit at best, and using all of the hypercores will make
jobs take longer overall. To determine the number of physical cores, you
can enter
imodqtassist -t
Parallel processing on multiple machines requires two things in addition
to a cpu.adoc file: it must be possible to log
in to all machines via ssh without a password, and the data must be in a
shared file system accessible to all machines.
To set up ssh keys for access without passwords, simply run
ssh-keygen -t rsa
and type Enter for all of the queries. Then enter:
cp $HOME/.ssh/id_rsa.pub
$HOME/.ssh/authorized_keys
If necessary, distribute this authorized_keys file to the .ssh directories
on other machines that do not have the same home directory. The three
different kinds of platforms (Linux/Unix, Mac OSX, Windows with Cygwin) may require
separately generated keys. If this seems to be the case, run ssh-keygen once
on each type of machine then
combine the .ssh/id_rsa.pub files from each into one authorized_keys file.
Distribute this combined authorized_keys file to the .ssh directories.
Processchunks runs jobs via ssh by starting a non-interactive bash login shell
on the remote computer. Any programs to be run must be on your path when
logging in as a bash user. If you use only IMOD programs in the command file
and IMOD has been installed by the default method, there should be no
problem and nothing else to do. The exception is on Ubuntu with an
older version of IMOD installed. Before IMOD 4.9, the installer did not
copy the IMOD startup scripts to /etc/profile.d, and the
the environment thus does not get set right for running commands
through ssh. The easiest remedy is to upgrade IMOD.
However, if you set up the IMOD environment in your own startup files instead
of in the default way, you need to make sure that the environment is defined
when running this bash shell. Specifically, you need to set the IMOD_DIR
environment variable then source $IMOD_DIR/IMOD-linux.sh or
$IMOD_DIR/IMOD-mac.sh in your ~/.bash_profile
and not just in your ~/.bashrc, since the latter is not run by the
non-interactive shell. Similarly, if you are running programs outside IMOD
whose environment is set up in your own startup files, you need to do
that in ~/.bash_profile. However, we have found that in
other contexts it does not work to set environment only
in ~/.bash_profile. Thus, the recommended approach is to
set the environment in ~/.bashrc and source that file
from ~/.bash_profile.
To diagnose problems, there are a few tests that you can run by issuing the
same kind of command that Processchunks uses to run jobs, of the form:
ssh -x machine bash --login -c \'"command"\'
where the command can be relatively complex because of the quoting; but the
quoting can be omitted for simple commands. Specifically, use
ssh -x machine bash --login -c \'"cd directory"\'
to test if you can change to the given directory. Use
ssh -x machine bash --login -c imodinfo
to test if the remote machine can run IMOD this way, and use
ssh -x machine bash --login -c env > env.out
to collect the environment if there is trouble running IMOD.
It is possible to have a user name as part of the machine name
(user@machine) in these ssh commands, in the cpu.adoc
file, or in the machine names provided when running Processchunks
directly. However, although the user name may be different between
machines, it should be the same user in some sense (probably in terms of
the user ID on the systems).
With most versions of the IMOD 4.11 packages, you can use the graphics processing unit (GPU) of an NVIDIA graphics card to compute tomograms, correct for microscope CTF, and align camera movie frames. This works with any recent NVIDIA card, but you also need to have NVIDIA drivers new enough to support the version of CUDA that IMOD was built with. To see if your card can be used, check it in NVIDIA's lists . Some of the packages for IMOD 4.11 are built with CUDA version 8. A few packages are built for older CUDA versions. A package built with a particular version of CUDA will work with CUDA drivers of the same or a higher version. Always use a package built with the highest version number supported by your drivers, because there may be a significantly longer startup time using a package built with a lower version (this is the case for CUDA 6). Here are details for the three operating systems:
The easiest way to test whether the GPU is functioning and computing reliably
is to run the command:
gputilttest
This will unpack test data and do a one-minute test for reproducibility.
And optional argument can be added to set the length of the test in minutes; an
optional second argument can be used to specify the GPU number when there is
more than one. Some years ago, a few cards gave variable results, so
it may be important
to test for reproducible results initially, periodically thereafter, and
especially after upgrading the NVIDIA drivers or the operating system.
There is also a button on the Front Page of Etomo for running this test.
If the test fails, the file gputtest.log will have some
diagnostic information, in particular a line like
CUDA version - driver: 6.050 runtime: 6.000
which would indicate a version problem if the driver is lower than the runtime.
The GPU can be enabled for use when making reconstructions in Etomo in one of two ways. If you have a cpu.adoc file to specify machines available for parallel processing, then you need to add a line
gpu = 1
to the section for each computer with a usable GPU. If you do not have a
cpu.adoc file, then select Settings from the Options menu
of Etomo. In the box User Level Enhanced Processing, check Enable
graphics processing. However, if there is more than one gpu in
your computer, the only way to access this is by providing
a cpu.adoc with a line like
gpu.device = 1,2,3
See the cpu.adoc help file for details
and the example cpu.adoc file in IMOD/autodoc.
If you want to know how much speed improvement your system has, get tilttimers.tar.gz
from our benchmark
directory and follow
the instructions in the README file there. More extensive
benchmarks are available in the file gputests.tar.gz.
Several parts of IMOD look for data and configuration files in a separate
location, pointed to by the environment variable IMOD_CALIB_DIR. These files
include the cpu.adoc file for enabling parallel processing,
distortion correction files, noise files for microscope CTF correction, and
local startup files. The default value for IMOD_CALIB_DIR is /usr/local/ImodCalib
on all platforms except Windows without Cygwin, where it is set to
C:\ProgramData\IMOD on Windows Vista and higher. It is set
in the IMOD startup scripts if it is not already defined. We have designed
this directory as a place for local files
that should not be replaced when IMOD is upgraded. Minimally, then, you may
want to create this directory and place a cpu.adoc there defining
the number of processors on one or more machines. In addition, the IMOD startup
scripts will try to source local startup scripts in this directory: IMOD-...csh
will source $IMOD_CALIB_DIR/IMOD.csh and IMOD-...sh will
source $IMOD_CALIB_DIR/IMOD.sh. You can use these startup scripts
for customizations, such as redefining IMOD_JAVADIR, instead of
modifying the startup scripts that come with IMOD and get replaced with each
new version. However, if you are going to take advantage of this mechanism and
want to redefine IMOD_CALIB_DIR to point to a different location,
your startup must set this environment variable before sourcing the IMOD
startup scripts.
To unpack a copy of IMOD for test purposes and run it in parallel with an installed copy, follow these steps except on Windows without Cygwin:
.sh), for example imod_4.12.10_win64_CUDA8.0.sh.
cd to the directory where you want this copy of IMOD
to be located and move the package file there.
testIMOD, run
sh imod_4.12.10_win64_CUDA8.0.sh -skip -dir . -name testIMOD
bash shell, run these commands in a
terminal any time you want to run this copy instead of the installed
one:
unset IMOD_DIR
unset IMOD_PLUGIN_DIR
source testIMOD/IMOD-*.sh
If running the tcsh shell, use unsetenv and
source the .csh file instead.
On Windows without Cygwin, follow these steps (which only work with
an installIMOD from an installed version of
4.9.11 or 4.10.21, or higher):
.sh instead
of .exe, for example imod_4.12.10_win64_CUDA8.0.sh.
cd to
the directory where you want this copy of IMOD to be located and move
the package file there, for example, C:\Users\myname\Documents.
testIMOD, run
python %IMOD_DIR%\installIMOD -skip -dir
. -name testIMOD imod_4.12.10_win64_CUDA8.0.sh
set IMOD_DIR=C:\Users\myname\Documents\testIMOD
PATH=%IMOD_DIR%\bin;%PATH
set IMOD_PLUGIN_DIR=%IMOD_DIR%\lib\imodplug
High-DPI (high-resolution) monitors are supported to varying extents in the three graphical programs in IMOD based on the Qt toolkit: 3dmod, midas, and ctfplotter. This support relies on the solutions provided by Qt, which are imperfect and vary between operating systems. They are only available in IMOD packages built with Qt 5: currently RHEL7 in Linux, packages for CUDA6.5 and CUDA 8.0 on Windows, and the osx10.11 package on Mac. On Windows and Mac, the support is dynamic: programs can detect when a window is moved between monitors with different DPI and adjust the font size and spacing in dialogs. On Linux, the scaling for DPI only works properly when set before program startup, so problems will be encountered when using monitors with different DPIs. These points may be helpful when using a high-DPI monitor:
Support for 16-bit floating point values in MRC files, such as those used in Relion and available in numpy, was added in IMOD 4.12.17. A new mode for these values, 12, is now part of the MRC standard, but other software may not support it yet. Numbers in this format have a precision of 10 bits, or 0.1%, down to values of 0.00006. From this value down to 6x10e-9 (the lowest non-zero value), there are 1023 values with a precision of 6x10e-9, i.e., they occur in steps of that size. The lowest and highest possible values are -65504 and 65504. This is adequate for many uses in EM.
All programs except one can read files in this mode. All of the programs that have an option to explicitly set the mode can produce output in this mode. Otherwise, the output mode will be 32-bit floats (mode 2) whenever the input is 16-bit floats. However, and environment variable, IMOD_WRITE_FLOATS_16BIT, can be set nonzero to make the default floating point output for all programs be 16-bit. This default will fully govern the behavior of programs without an option to set the output mode. For the programs with an option, the default is overridden by whatever mode is specified with the option.
You will want to go through the Introduction to 3dmod
because 3dmod is the central graphical tool of the IMOD
package. If you are doing tomography, you should start with the
Etomo tutorial. This Etomo tutorial is also available in video
form on our YouTube channel.
If you are doing reconstructions from serial images such as serial thin
sections or serial block face images, you should work through the
Serial Section Alignment guide, which
will take you through the steps needed to align the images in Etomo.
For access to the complete IMOD documentation, just enter imodhelp
at the command line to open it in the Qt Assistant, where it can be browsed and
searched.
Aside from learning to use the major tools, your initial problem may be getting data into a format usable by the IMOD programs. If you are having problems getting your data into a format usable by IMOD contact, us for help.
All of the IMOD programs read and produce files in
the MRC image file format. All but one
can read and produce files in an HDF image file
format compatible with EMAN2; HDF files
from UCSF Chimera can also be read.
Programs can also read and write TIFF image stacks and single-image JPEG
files, and can read files in several specialized
image formats compatible with MRC: DigitalMicrograph, PIF files from
Bsoft, EM, Hanspeter Winkler's NFF, and FEI/TFS raw files.
In addition to those formats, 3dmod can read some other common
formats like PNG and BMP,
and it has a dialog box and options for specifying how to read raw
data.
As of IMOD 4.9, programs write MRC files in byte mode as signed by default (values of -128 to 127), which was a change from previous behavior to conform with a clarification of the MRC standards. Such files will not be read correctly by IMOD versions before 4.3, and you may still encounter other software that has difficulty with signed byte files. Two programs have command-line options to produce unsigned output files (values 0-255): newstack (option "-byte 0") and clip (option "-m ubyte"). In addition, you can make all programs write unsigned bytes by setting the environment variable WRITE_MODE0_SIGNED to 0. At least as of version 2.1.0/1.53g, ImageJ does not read signed byte files correctly unless you import them through the Bioformats tool. Please inform the IMOD developers if you run into other up-to-date software that does not read signed bytes correctly.
Even though IMOD programs can read multiple file types, you will generally want to convert your data to a stack of images in MRC or HDF format, because most programs are designed to operate on a stack of images in a single file rather than on a set of single-image files. Thus, we have utility programs available for converting TIFF files and raw data into the MRC file format and combining single-image files into a stack.
Use the program tif2mrc to convert a series
of TIFF image files into a single MRC image file. The tif2mrc program
has an option for converting 24-bit color to 8-bit grayscale images. The
following example entry will create a MRC file from a list of TIFF files
(cell01.tif, cell02.tif ...).
tif2mrc cell*.tif cell.mrc
The files must be in the current directory of the terminal where you
enter the command. See the tif2mrc
manual page for more information on how to
use tif2mrc.
Use the program dm2mrc to convert a series of
DigitalMicrograph image files into a single MRC image file. The following
example will create a MRC file from a list of DigitalMicrograph files
(cell01.dm3, cell02.dm3....; note that dm2 and dm4 files are also
supported.)
dm2mrc
cell*.dm3 cell.mrc
If you have a series of MRC files, with one image per file, you can
combine them into a single stack easily with the program newstack.
For example, enter
newstack cell*.mrc cell.st
You can also use newstack to stack TIFF and
DigitalMicrograph files, provided that no special conversion options are
needed. newstack and another
program clip, have options for specifying that the output
should be in HDF format; other programs can be made to do so by setting
an environment variable, IMOD_OUTPUT_FORMAT (see
the page on environment variables).
The program raw2mrc is used to convert raw
image data into the mrc format. This program can take a file of 8, 16,or 32 bit
integers, IEEE float values, or 24-bit RGB triplets and convert them into an
MRC image file. In MRC files, the data start in the lower left hand corner of
the image, with the data stored in rows. To use raw2mrc, you need
to know the size of the images, the type of data, and the size of any header
information preceding the image. For example, if you have a set of files
(cell01.em, cell02.em, ...) with 1024 x 1024 images of signed 16-bit integers,
and a header of 512 bytes, use:
raw2mrc -t short -x 1024 -y 1024 -o 512 cell*.em cell.mrc
If the data need to have their bytes swapped because they come from a very old machine with the opposite byte ordering, use the -s option. If you do not know something about the image, such as the header size or whether the data are unsigned or need swapping, you may be able to figure it out just by trying different options for data types and swapping. If you do not know the header size, convert one file without the -o option, load it into 3dmod, and try to see where the image data start. If the final MRC image is upside down use the -f option in the initial conversion or use the program clip to flip the image back.
When a 3dmod is started with an image file that
it does not recognize, it brings up a dialog that allows you to specify the
image and header size and the data type. Alternatively, you can specify
these features with options at the command line, which could be the most
convenient way to experiment and find the right values. For example, the
files in the previous command could be displayed with:
3dmod -r 1024,1024,1 -H 512 -t 1 cell*.em
If you already have a 3-D model and wish to view it within the IMOD model
viewing program, 3dmodv, you will need to convert the file into
the IMOD format. See the IMOD model file format ASCII
and binary specifications if you wish to write
your own conversion program.
The IMOD model format can be either binary or ASCII.
The main
use of the ASCII format would be to access the data for analysis or conversion
by other programs. To convert a binary IMOD file (binary.imod) to an ASCII IMOD
file (ascii.imod) use the imodinfo command:
imodinfo -a binary.imod > ascii.imod
or
imodinfo -a -f ascii.imod binary.imod
will both create an ASCII model file from the binary.imod model. The ASCII format preserves many but not all possible features in the model. It is moderately complex and may not be the most convenient format to use for exporting or importing data. There are also two programs, model2point and point2model, that can be used to convert an IMOD model to or from a simple list of point coordinates.
In order to get accurate information the fields in the model header have to be set properly. See the Introduction to 3dmod for an explanation of how to do this. Selecting the Edit->Contour->Info menu item from the 3dmod Information Window will cause some quantitative information to be printed out in the bottom panel of the window.
Use the imodinfo command to get basic
information from a model and print it out to a terminal or file. For example:
imodinfo cell.imod
# MODEL cell.imod
# NAME A little cell
# PIX SCALE: x = 1
# y = 1
# z = 9.17
# PIX SIZE = 0.00654
# UNITS: um
OBJECT 1
NAME: spindle pole
5 contours
object uses closed contours.
color (red, green, blue) = (0, 1, 1)
CONTOUR #1,2,0 16 points, length = 0.464513, area = 0.0134249
CONTOUR #2,2,0 14 points, length = 0.458311, area = 0.0125642
CONTOUR #3,2,0 8 points, length = 0.200755, area = 0.00277481
CONTOUR #4,2,0 13 points, length = 0.313501, area = 0.00664029
CONTOUR #5,2,0 9 points, length = 0.232374, area = 0.00272134
Total volume = 0.00228646
Total contour cylinder surface area = 0.10012.
Total mesh surface area = 0.0349499.
There are several useful command line options for imodinfo to extract lengths of contours into a single column output, print surface and point size information, and compute volumes and mesh areas. A text file can be created using the -f option.
IMOD models can be converted to a few other 3rd party formats. Perhaps the only one currently useful is Virtual Reality Modeling Language: imod2vrml converts to VRML 1.0; and imod2vrml2 converts to VRML 2. VRML has been superceded by X3D.
See also: Manual pages for 3dmodv, imodmesh, and imodinfo.
This list shows only the most important of the many documents in
IMOD. A complete set of links to all of the documention can be found in
two places:
Index file with links
to all files in the current set of documentation being viewed.
Web page
section with links to all documentation in either the current stable release
or beta version of IMOD, as well as links for downloading tutorial data sets.