Tomo3DEM

Tomo3DEM is a software suite for in situ structural analysis of the subcellular architecture and molecular organization of cells and tissues, by efficiently processing tomographic volumes from the different modalities of three-dimensional Electron Microscopy (3DEM), with special emphasis on (cryo-)electron tomography (cryoET) and (cryo-)volume EM with FIB-SEM. It comprises a set of independent standalone programs that provide functionality complementary to other well-established software and workflows in the 3DEM field.

Electron tomography

• TomoCTF: CTF determination and correction in electron cryotomography.
• TomoAlign: tilt-series alignment and tomographic reconstruction that deals with beam-induced sample motion and 3D-CTF correction in cryoET.
• MaskTomRec: removes contamination-induced reconstruction artefacts in cryo-electron tomograms from FIB-milled samples.
• Tomo3D: fast tomographic reconstruction (WBP and SIRT) on standard multicore computers.
• TomoAND / TomoEED: fast 3D denoising in cryoET with Anisotropic Non-linear Diffusion (Edge-Enhancing Diffusion mode).
• TomoDENOISE: fast 3D feature-preserving noise filtering (linear, nonlinear and anisotropic methods).
• TomoBlob: detection and picking of blob-like features in (cryo-)ET.
• TomoSegMemTV: robust membrane segmentation based on Tensor Voting.
• TomoSpatStat: spatial and nearest-neighbour statistical analysis of structures in (cryo-)ET.
• RANSAC: outlier detection and angular constraining in subtomogram alignment of filament-like structures.
• Scipion plugins for Tomo3D and TomoSegMemTV.

FIB-SEM tomography

• polishEM: image enhancement and sharpening of FIB-SEM stacks, including correction of curtaining artefacts.
• IsoFlow: generation of isotropic FIB-SEM stacks by optical-flow interpolation.
• FlowDenoising: structure-preserving noise reduction in FIB-SEM stacks driven by optical flow.
• MitoStats: analysis of mitochondrial networks in 3DEM, in combination with MitoGraph.

Single-particle electron cryo-microscopy

• EM-Bfactor: B-factor estimation and sharpening of high-resolution information in cryoEM maps.

Scientific computing

• Oddylos: on-demand dynamic load scheduler for hybrid CPU+GPU computing systems.
• spmvELLRT: library for efficient sparse matrix-vector product on GPUs.