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:
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
The integrated protocols are:
- tomo3d - denoise tomograms
- tomo3d - reconstruct tomograms
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
- 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.
If you experiment any problem, please contact us here: scipion-users@lists.sourceforge.net, scipion@cnb.csic.es or open an issue.
We'll be pleased to help.
Scipion Team