About
The Segmentation Annotation Tool (SAT) is an online tool designed to simplify the process of annotating EMDB Segmentation File Format (EMDB-SFF) files. EMDB-SFF is a community-driven, open file format for segmentation and subtomogram average data exchange. You can read more about EMDB-SFF at its main documentation page.
In order to use SAT you will need to have an existing segmentation in one of the supported application-specific segmentation file formats which you will then convert to an EMDB-SFF file.
Supported application-specific segmentation file formats supported are:
- Amira Mesh (*.am, *.elm, *.lmb)
- Amira HyperSurface (*.surf)
- CCP4/CCP-EM Masks (*.map, *.mrc, *.rec)
- ilastik (*.h5)
- IMOD (*.mod)
- Segger (*.seg)
- Stereolithography (STL) (*.stl)
- SuRVoS (*.h5) (**preliminary support)
EMDB-SFF files contain two types of data:
- segmentation geometries specified using either mesh, shape or volume primitives, and annotations (or simply notes), which are references to accessions pertaining to publicly accessible ontological terms and related datasets.
- SAT is concerned with textual annotations i.e. addition of the annotations to EMDB-SFF files. Annotation can also be done using sfftk (see sfftk: Alternative to SAT for how to do this).