3DEM image processing software

Tomo3DEM is a software suite for efficiently processing tomographic volumes from the different modalities of three-dimensional Electron Microscopy (3DEM), with special emphasis on cryo-ET and volume EM with FIB-SEM. 

Tomo3DEM comprises a set of independent standalone programs that intend to provide a functionality complementary to other well-established software and workflows in the 3DEM field.

Selected recent major publications that made use of Tomo3DEM programs: 

Cell 2023 (Tomo3D, TomoCTF), Cell 2023 (MaskTomRec), Science 2023 (Tomo3D), Nature Nanotechnology 2023 (TomoCTF), Nature Microbiology 2023 (Tomo3D), Nature Methods 2023 (TomoAND/TomoEED), Science Advances 2023 (Tomo3D), Science Advances 2023  (MaskTomRec), Nature 2022 (TomoSegMemTV), Nature 2022 (TomoSegMemTV),  Nature Communications 2022 (Tomo3D)

Single particle electron cryo-microscopy

B-factor estimation and correction


Package for sharpening high resolution information in single particle electron cryomicroscopy

Discontinued stuff  (or previous versions)

People interested in the following packages should request them by email.

Tomographic Reconstruction

TOMO3D 2.0

Package for fast tomographic reconstruction on standard multicore computers

TOMO3DGPU    -   tomo3dgpu.pdf

Package for matrix tomographic reconstruction on GPUs

TOMO3Dhybrid     -    tomo3dhybrid.pdf

Package for fast tomographic reconstruction with CPU+GPU co-processing


TOMOAND 1.0    -    tomoand_1.0.pdf

Package for noise reduction in electron cryotomography with anisotropic nonlinear diffusion


Package for fast denoising of tomographic volumes based on Anisotropic Non-linear Diffusion (AND)


TOMOSEGMEM    -    tomosegmem.pdf

Package for segmentation of membranes in tomograms

CTF Determination in single particle cryoEM

EMCTF    -    emctf.pdf

Package for CTF determination of non-astigmatic images in electron cryomicroscopy