scipion-em-tomo3d 3.1.1

tomo3d and other software at https://sites.google.com/site/3demimageprocessing/Home ready to use in scipion.

Scipion plugin for Tomo3D

This plugin allows to use some of the software packages from 3demimageprocessing within the Scipion framework. The binaries for the plugin MUST be downloaded manually:

Setup - Binaries manual installation

The following binaries are used by tomo3d protocols. All of them can be found in 3demimageprocessing. These are:

• tomo3d

• tomobflow

• tomoeed

To get each of them, click on the corresponding link and fill the form located at the bottom of the displayed webpage. Once all of them have been downloaded, place them in scipionDirectory/software/em/tomo3d-VersionNumber.Thus, the final file structure expected by Scipion should look like this, being the listed files below the binaries or a link pointing to each:

scipionDirectory/software/em/tomo3d-VersionNumber

• tomo3d

• tomobflow

• tomoeed

Installation

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

1. User (stable) version::

scipion installp -p scipion-em-tomo3d

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

• Clone the source code repository:

git clone https://github.com/scipion-em/scipion-em-tomo3d.git

• Install:

scipion3 installp -p local/path/to/scipion-em-tomo3d --devel

Protocols

The integrated protocols are:

1. tomo3d - denoise tomograms

2. tomo3d - reconstruct tomograms

Tests

The installation can be checked out running some tests:

scipion3 tests tomo3d.tests.test_protocol_reconstruct_tomogram

scipion3 tests tomo3d.tests.test_protocol_denoise_tomogram

References

• Fast tomographic reconstruction on multicore computers. J.I. Agulleiro, J.J. Fernandez. Bioinformatics 27:582-583, 2011.

• Tomo3D 2.0 – Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction. J.I. Agulleiro, J.J. Fernandez. Journal of Structural Biology 189:147-152, 2015.

• TOMOBFLOW: feature-preserving noise filtering for electron tomography. J.J. Fernandez. BMC Bioinformatics 2009, 10:178.

• TomoEED: Fast Edge-Enhancing Denoising of Tomographic Volumes. J.J. Moreno, A. Martinez-Sanchez, J.A. Martinez, E.M. Garzon, J.J. Fernandez. Bioinformatics 34:3776-3778, 2018.

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