Tomo3DEM
3DEM image processing software
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:
Nature Microbiol 2025 (Tomo3D), Nature Biomed Eng 2025 (TomoAlign), Nature 2024 (Tomo3D), Nature 2024 (Tomo3D), Science 2024 (Tomo3D, TomoSegMemTV), Nature Cell Biol 2024 (MaskTomRec), Nature Communications 2024 (FlowDenoising), Cell 2023 (Tomo3D, TomoCTF), Cell 2023 (MaskTomRec), Science 2023 (Tomo3D), Nature Nanotechnology 2023 (TomoCTF), Nature Methods 2023 (TomoAND/TomoEED), Science Advances 2023 (MaskTomRec), Nature 2022 (TomoSegMemTV), Nature 2022 (TomoSegMemTV), Nature 2021 (Tomo3D), Cell 2021 (TomoSegMemTV), Cell 2021 (TomoSegMemTV), Science 2021 (Tomo3D), Cell 2020 (TomoSegMemTV)
CTF Determination and Correction
Package for CTF determination and correction in electron cryotomography
Tilt-series Alignment and Tomographic Reconstruction with Motion Correction and 3D-CTF Correction
Package to deal with beam-induced sample motion and 3D-CTF in cryoET
Tomographic Reconstruction
Package for removing contamination-induced reconstruction artefacts in cryo electron tomograms from FIB-milled samples
Package for fast tomographic reconstruction on standard multicore computers
Denoising
Package for fast 3D denoising in cryoET with Anisotropic Non-linear Diffusion (AND)
Packages for fast 3D feature-preserving noise filtering (linear, nonlinear and anisotropic methods)
Segmentation and Feature detection
Package for detection of blob-like features in (cryo-)ET.
Package for robust membrane segmentation based on Tensor Voting
Interpretation
Package for spatial and neighbour analysis in (cryo-)ET.
Subtomogram Averaging
Package for outlier detection and angular constraining in subtomogram alignment.
Scipion plugin
Image enhancement
Package for image enhancement and sharpening in FIB-SEM Tomography.
Image interpolation
Package for generating isotropic FIB-SEM stacks by Optical Flow.
Denoising
Package for structure-preserving noise reduction in FIB-SEM stacks.
Interpretation
B-factor estimation and correction
Package for sharpening high resolution information in single particle electron cryomicroscopy
People interested in the following packages should request them by email.
Tomographic Reconstruction
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
Denoising
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)
Package for feature-preserving noise filtering in electron tomography
Segmentation
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