EMDB-SFF Toolkit (sfftk)
Introduction
sfftk is a set of utilities that facilitate creation, conversion and modification of Electron 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.
Audience
sfftk is primarily targeted but not restricted to biological electron microscopists and developers of image segmentation software.
License
sfftk is 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 Model
sfftk is built to handle EMDB-SFF files. The corresponding schema (v0.8.0.dev1) may be found at https://emdb-empiar.github.io/EMDB-SFF. Changes to the schema are welcome for discussion at the Segmentation Working Group at https://listserver.ebi.ac.uk/mailman/listinfo/segtrans-wg.
Supported Formats
The 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 RELION
Stereolithography (.stl)
Amira HyperSurface (.surf)
Contact
Any questions or comments should be addressed to pkorir at ebi dot ac dot uk.
Publications
The EMDB-SFF data model is the result of various community consultations which are published in the following articles:
Getting Started
Obtaining and Installing sfftk
Dependencies
As with any Python software, we recommend installing it in a virtual environment (of your choice). The only dependency that may be needed is numpy which can be installed with
pip install numpyPyPI
sfftk is available on PyPI meaning that all that one needs to do is run:
pip install sfftkSource
The sfftk source is available from Github https://github.com/emdb-empiar/sfftk.
Features
sfftk has two principal functions:
convert application-specific segmentation file format (AS-SFF) files to EMDB-SFF;
annotate EMDB-SFF files against known ontologies.
Conversion
Segmentation files may be converted to EMDB-SFF files using the convert command.
sff convert file.am -o file.sffFor a full description of how to perform conversion, please see the guide to format conversion.
Annotation
Annotation is performed using the notes utility on EMDB-SFF files.
sff notes show -H file.sffsfftk provides a simple set of tools to allow viewing, searching and modifying annotations associated 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 the guide to annotating segmentations for a full treatment.
Miscellaneous
sfftk may also be used for several miscellaneous operations such as:
Prepping segmentations before conversion to EMDB-SFF
Setting configurations that affect how sfftk works
Running unit tests with the tests command
More information on this can be found in the guide to miscellaneous operations.
Developing with sfftk
sfftk is developed as a set of decoupled packages providing the various functionality. The main classes involved are found in the sfftkrw package. There is also a guide to developing with sfftk which provides useful instructions.
Extending sfftk
sfftk has built with extensibility in mind. It is anticipated that most extension will take the form of supporting additional file formats. Please read the guide to extending sfftk to learn how to do this.
1 maintainer
Release files for sfftk 0.10.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| sfftk-0.10.3.tar.gz | 143.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| sfftk-0.10.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 471.7 kB
Release files / sfftk-0.10.3.tar.gz
| Download URL | sfftk-0.10.3.tar.gz |
|---|---|
| Size | 143.9 kB |
| Tags | Source |
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Release files / sfftk-0.10.3-py3-none-any.whl
| Download URL | sfftk-0.10.3-py3-none-any.whl |
|---|---|
| Size | 327.7 kB |
| Tags | Python 3 |
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