Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy, designed and managed by the Biocomputing Unit located in Madrid, Spain.
The Xmipp project is divided into four repositories. This is the main repository, which contains the majority of the source code for the programs, additional scripts, and tests. Three remaining repositories, XmippCore, XmippViz, and Scipion-em-xmipp, are automatically downloaded during the installation process.
To have a complete overview about Xmipp please visit the documentation web. The recommended way for users (not developers) to install and use Xmipp is via the Scipion framework, where you can use Xmipp with other Cryo-EM-related software.
Mind that for this command to succeed, all dependencies need to be pre-installed and findable by Xmipp. When using non-standard install directories, this needs to be indicated to Xmipp though the Scipion configuration file. See Software dependency section for further details. To correctly interoperate with CUDA, please visit the official installation guide of Scipion.
Once Scipion is in working order, launch the Xmipp Plugin installer with
scipion3 installp -p scipion-em-xmipp
By default this will employ all CPU cores available in the system for compilation. If this is not the desired behavior, please consider using -j <N> flag to limit the amount of CPU cores.
For developers, it becomes handy to install Xmipp in an external directory for easy integration with IDEs. By default Xmipp installer takes care of linking to Scipion.
The first step is to download Xmipp sources:
git clone https://github.com/I2PC/xmipp.git
cd xmipp
If you want to checkout an scpecific branch use the following command. For repositories where the branch does not exist, devel is utilized.
./xmipp getSources -b branch
Compile Xmipp
scipion3 run ./xmipp
Refer to ./xmipp --help for additional info on the compilation process and possible customizations.
Install the Scipion plugin.
scipion3 installp -p src/scipion-em-xmipp/ --devel
Xmipp is installed in the build directory located in the same directory where the xmipp script is located. To set all necessary environment variables and paths to all Xmipp programs, you can simply run source dist/xmipp.bashrc.
We have tested Xmipp compilation on the following operating systems: Ubuntu 18.04, Ubuntu 20.04, Ubuntu 22.04, Centos 7. Visit the OS wiki page for more details.
While compilation and execution might be possible on other systems, it might not be straightforward. If you encounter a problem, please refer to known and fixed issues. Let us know if something is not working.
At least 2 processors are required to run Xmipp. In some virtual machine tools only one is assigned, please check that at least two processors are assigned to the virtual machine
Note that these dependencies are installed by default though conda (except for CUDA). Only install them externally when required.
Xmipp requires C++17 compatible compiler (see table below for minimum versions). We have had good experience with using GCC. Clang is mostly untested. Mind that when compiling with CUDA, a compatible compiler must be installed and findable (although it may not be used for non-CUDA sources) for Xmipp.
| Compiler | Minumum version |
|---|---|
| GCC | 8.4 |
| Clang | 5.0 |
Xmipp requires CMake 3.17 or above. To update it please visit the dedicated section in the Wiki.
Xmipp supports CUDA 10.2 through 12.2. CUDA is optional but highly recommended. We recommend you to use the newest version available for your operating system. Some Xmipp programs are only compiled if CUDA 11 is available. Pay attention to the compiler - CUDA compatibility.
To install CUDA for your operating system, follow the official install guide.
sudo apt install -y libfftw3-dev libopenmpi-dev libhdf5-dev python3-numpy python3-dev libtiff5-dev libjpeg-dev libsqlite3-dev default-jdk git cmake gcc-10 g++-10
Note: For HDF5 to be available Extra Packages for Enterprise Linux (EPEL) repository needs to be activated in certain distros with
yum install epel-release
Note: On CentOS-7 the gcc available by default is not compatible with Xmipp. You can enable newer gcc releases using:
yum install centos-release-scl
yum install devtoolset-10
scl enable devtoolset-10 bash
yum install python3-devel python3-numpy fftw-devel openmpi-devel hdf5-devel sqlite-devel libtiff-devel libjpeg-turbo-devel java-17-openjdk-devel git cmake gcc g++
If you miss some feature or find a bug, please create an issue and we will have a look at it, you can also contact us by [email protected]. For more details, troubleshootings and information visit the wiki page.
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