scipion-em-tomosegmemtv 3.1.0

Scipion plugin tomosegmemtv.

Scipion - TomoSegMemTV plugin

Scipion plugin for segmentation and annotation of membranes in tomograms (with TomoSegmenTV and memb-annotator, respectively)

Installation

The plugin can be installed in user (stable) or developer (latest, may be unstable) mode:

1. User (stable) version::

scipion3 installp -p scipion-em-tomosegmemtv

2. Developer (latest, may be unstable) version::

• Clone the source code repository:

git clone https://github.com/scipion-em/scipion-em-tomosegmemtv.git

• Install:

scipion3 installp -p local/path/to/scipion-em-tomosegmemtv --devel

Getting the binaries for tomoSegmenTV

TomoSegmenTV binaries must be downloaded from the following site https://sites.google.com/site/3demimageprocessing/tomosegmemtv, where a form must be filled and submitted to get instant download access. Download the standalone version (which will be a zip file), unzip it and move the binary file to the directory SCIPION_HOME/software/em/TOMOSEGMEMB_DIRECTORY/tomoSegMemTV/bin/. It can be directly done executing the following command on a terminal:

cd DOWNLOADED_FILE_DIRECTORY

unzip DOWNLOADED/FILE -d SCIPION_HOME/software/em/TOMOSEGMEM_DIRECTORY/tomoSegMemTV/bin/

Protocols

The integrated protocols are:

1. tomosegmemtv - annotate segmented membranes: Manual annotation tool for segmented membranes.

2. tomosegmemtv - resize segmented or annotated volume: Resize segmented volumes or annotated (TomoMasks).

3. tomosegmemtv - tomogram segmentation: segment membranes in tomograms.

Tests

The installation can be checked out running some tests (Important: test_resize_tomomask requires the plugin scipion-em-imod to be installed).

scipion3 tests tomosegmemtv.tests.test_tomosegmemtv

scipion3 tests tomosegmemtv.tests.test_resize_tomomask

Tutorial

A tutorial about how to use tomosegmemtv and the membrane annotator within Scipion can be found here.

References

• Robust membrane detection based on tensor voting for electron tomography.

  A. Martinez-Sanchez, I. Garcia, S. Asano, V. Lucic, J.J. Fernandez. Journal of Structural Biology 186:49-61, 2014.

Contact information

If you experiment any problem, please contact us here: [e-mail], [e-mail] or open an issue.

We’ll be pleased to help.

Scipion Team