Package: sfftk
ContentsIntroductionAudienceLicenseData ModelSupported FormatsContactPublicationsGetting StartedDependenciesPyPISourceFeaturesConversionAnnotationMiscellaneousDeveloping withsfftkExtendingsfftkIntroductionsfftkis a set of utilities that facilitate creation, conversion and
modification ofElectron Microscopy Data Bank - Segmentation File Format
(EMDB-SFF) files.
EMDB-SFF is an open, community-driven file format to handle annotated
segmentations and subtomogram averages that facilitates segmentation file
interchange. It is written in Python and provides both a command-line
suite of commands and a Python API.Audiencesfftkis primarily targeted but not restricted to biological electron
microscopists and developers of image segmentation software.Licensesfftkis free and open source software released under the terms of the Apache License, Version 2.0. Source code is
copyright EMBL-European Bioinformatics Institute (EMBL-EBI) 2017.Data Modelsfftkis built to handle EMDB-SFF files. The corresponding schema
(v0.8.0.dev1) may be found athttps://emdb-empiar.github.io/EMDB-SFF.
Changes to the schema are welcome for discussion at theSegmentation Working Groupathttps://listserver.ebi.ac.uk/mailman/listinfo/segtrans-wg.Supported FormatsThe following file formats are currently supported (in alphabetical order of
extensions):Amira Mesh (.am)SuRVoS (.h5; experimental support)CCP4 Masks (.map)IMOD (.mod)Segger (.seg)STAR (.star) for subtomogram averages produced using RELIONStereolithography (.stl)Amira HyperSurface (.surf)ContactAny questions or comments should be addressed topkorir at ebi dot ac dot uk.PublicationsThe EMDB-SFF data model is the result of various community consultations which
are published in the following articles:Patwardhan, Ardan, Robert Brandt, Sarah J. Butcher, Lucy Collinson, David Gault, Kay Grünewald, Corey Hecksel et al. Building bridges between cellular and molecular structural biology. eLife 6 (2017).Patwardhan, Ardan, Alun Ashton, Robert Brandt, Sarah Butcher, Raffaella Carzaniga, Wah Chiu, Lucy Collinson et al. A 3D cellular context for the macromolecular world. Nature structural & molecular biology 21, no. 10 (2014): 841-845.Patwardhan, Ardan, José-Maria Carazo, Bridget Carragher, Richard Henderson, J. Bernard Heymann, Emma Hill, Grant J. Jensen et al. Data management challenges in three-dimensional EM. Nature structural & molecular biology 19, no. 12 (2012): 1203-1207.Getting StartedObtaining and InstallingsfftkDependenciesAs with any Python software, we recommend installing it in a virtual environment (of your choice). The only dependency
that may be needed isnumpywhich can be installed withpipinstallnumpyPyPIsfftkis available on PyPI meaning that all that one needs to do is run:pipinstallsfftkSourceThesfftksource is available from Githubhttps://github.com/emdb-empiar/sfftk.Featuressfftkhas two principal functions:convertapplication-specific segmentation file format (AS-SFF) files to EMDB-SFF;annotateEMDB-SFF files against known ontologies.ConversionSegmentation files may be converted to EMDB-SFF files using theconvertcommand.sffconvertfile.am-ofile.sffFor a full description of how to perform conversion, please see theguide to format conversion.AnnotationAnnotation is performed using thenotesutility on EMDB-SFF files.sffnotesshow-Hfile.sffsfftkprovides a simple set of tools to allowviewing, searching and
modifying annotationsassociated with the segmentation and individual
segments. The added annotations should be either from a public ontology or be
an accession from a public database.See theguide to annotating segmentationsfor a full
treatment.Miscellaneoussfftkmay also be used for several miscellaneous operations such as:Viewing segmentation metadataPrepping segmentationsbefore conversion to EMDB-SFFSetting configurationsthat affect howsfftkworksRunning unit testswith thetestscommandMore information on this can be found in theguide to miscellaneous operations.Developing withsfftksfftkis developed as a set of decoupled packages providing the various
functionality. The main classes involved are found in thesfftkrwpackage.
There is also aguide to developing with sfftkwhich
provides useful instructions.Extendingsfftksfftkhas built with extensibility in mind. It is anticipated that most
extension will take the form of supporting additional file formats. Please
read theguide to extending sfftkto learn how to do
this.