Metadata-Version: 1.2
Name: scipion-em-susantomo
Version: 3.0b1
Summary: Plugin to use SUSAN within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-susantomo
Author: Grigory Sharov
Author-email: sharov.grigory@gmail.com
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-susantomo/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-susantomo/
Description: ============
        SUSAN plugin
        ============
        
        This plugin provides wrappers for `Susan <https://github.com/rkms86/SUSAN>`_ software: subtomogram averaging (StA) workflow for CryoET based on sub-stacks of images instead of sub-volumes of tomograms.
        SUSAN uses substacks that are cropped on-the-fly from the aligned tilt-series stack and performs the CTF correction according to the selected operation (alignment or reconstruction). With this approach we decrease the
        computational resources needed in a typical subtomogram averaging pipeline, as we no longer need the CTF corrected stacks, the full tomogram reconstructions, or all the subtomograms in multiple binning
        stages.
        
        .. image:: https://img.shields.io/pypi/v/scipion-em-susantomo.svg
                :target: https://pypi.python.org/pypi/scipion-em-susantomo
                :alt: PyPI release
        
        .. image:: https://img.shields.io/pypi/l/scipion-em-susantomo.svg
                :target: https://pypi.python.org/pypi/scipion-em-susantomo
                :alt: License
        
        .. image:: https://img.shields.io/pypi/pyversions/scipion-em-susantomo.svg
                :target: https://pypi.python.org/pypi/scipion-em-susantomo
                :alt: Supported Python versions
        
        .. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-susantomo?server=https%3A%2F%2Fsonarcloud.io
                :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-susantomo
                :alt: SonarCloud quality gate
        
        .. image:: https://img.shields.io/pypi/dm/scipion-em-susantomo
                :target: https://pypi.python.org/pypi/scipion-em-susantomo
                :alt: Downloads
        
        Installation
        -------------
        
        You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
        
        a) Stable version
        
        .. code-block::
        
           scipion installp -p scipion-em-susantomo
        
        b) Developer's version
        
           * download repository
        
            .. code-block::
        
                git clone -b devel https://github.com/scipion-em/scipion-em-susantomo.git
        
           * install
        
            .. code-block::
        
               scipion installp -p /path/to/scipion-em-susantomo --devel
        
        - SUSAN sources will be downloaded and compiled automatically with the plugin, but you can also link an existing installation. Default installation path assumed is ``software/em/susan-0.1``, if you want to change it, set *SUSAN_HOME* in ``scipion.conf`` file to the folder where the SUSAN is installed.
        - SUSAN installation requires CUDA libraries, gcc >= 9.x and cmake 3.22.x. OpenMPI is optional amd only required for running SUSAN on more than one cluster node. MATLAB is not required as this plugin uses Python API.
        - If you need to use CUDA different from the one used during Scipion installation (defined by *CUDA_LIB*), you can add *SUSAN_CUDA_LIB* variable to the config file.
        - If you have to use a MPI for SUSAN different from Scipion MPI, you can set *SUSAN_MPI_BIN* and *SUSAN_MPI_LIB* variables in the config file. At the moment MPI support in the plugin is not working.
        
        
        Verifying
        ---------
        
        To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing ``scipion test --show --grep susantomo``
        
        Supported versions
        ------------------
        
        0.1
        
        Protocols
        ----------
        
        * ctf estimation
        * multi-reference alignment
        * average and reconstruct
        * create a subset
        
        References
        -----------
        
        1. Sánchez RM, Mester R, Kudryashev M. Fast Cross Correlation for Limited Angle Tomographic Data. In: Felsberg M., Forssén PE., Sintorn IM., Unger J. (eds) Image Analysis. SCIA 2019. Lecture Notes in Computer Science, vol 11482. Doi: 10.1007/978-3-030-20205-7_34
        2. R.M. Sánchez, R. Mester and M. Kudryashev. Fast Alignment of Limited Angle Tomograms by projected Cross Correlation. 2019 27th European Signal Processing Conference (EUSIPCO), 2019, pp. 1-5, doi: 10.23919/EUSIPCO.2019.8903041
        
Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
