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    49 repositories

    • torch-motion-correction

      Public
      Motion estimation and correction for cryo-EM images in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•2•1•Updated Aug 4, 2025Aug 4, 2025

    • teamtomo.github.io

      Public
      teamtomo.org website
      CSS
      •3•1•0•0•Updated Aug 3, 2025Aug 3, 2025

    • torch-segment-membranes-3d

      Public
      Semantic segmentation of membranes in cryo-ET data using a pre-trained network
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•1•1•Updated Aug 1, 2025Aug 1, 2025

    • torch-cubic-spline-grids

      Public
      Cubic spline interpolation on multidimensional grids in PyTorch
      Python
      •
      Other
      •4•32•3•1•Updated Jul 25, 2025Jul 25, 2025

    • torch-tiltxcorr

      Public
      Coarse tilt series alignment in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•1•0•Updated Jul 25, 2025Jul 25, 2025

    • torch-fourier-slice

      Public
      Fourier slice extraction/insertion in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•3•3•0•Updated Jul 22, 2025Jul 22, 2025

    • torch-tomogram

      Public
      (sub-)Tomogram reconstruction, subtilt extraction for cryo-ET.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•2•0•Updated Jul 21, 2025Jul 21, 2025

    • mdocfile

      Public
      SerialEM mdoc files as pandas dataframes
      Roff
      •
      BSD 3-Clause "New" or "Revised" License
      •8•13•2•0•Updated Jul 20, 2025Jul 20, 2025

    • ttsim3d

      Public
      Simulate a 3D scattering potentials from PDB files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•1•0•Updated Jul 20, 2025Jul 20, 2025

    • torch-ctf-estimation

      Public
      local defocus estimation in cryo-EM images
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Jul 20, 2025Jul 20, 2025

    • torch-fourier-filter

      Public
      Fourier space filters for 2D/3D data in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•1•0•Updated Jul 19, 2025Jul 19, 2025

    • teamtomo-runner-test

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • membrain-seg

      Public
      membrane segmentation in 3D for cryo-ET
      Python
      •
      Other
      •16•79•14•3•Updated Jul 19, 2025Jul 19, 2025

    • torch-segment-fiducials-2d

      Public
      Semantic segmentation of gold fiducial markers in cryo-EM images in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•0•0•Updated Jul 14, 2025Jul 14, 2025

    • torch-grid-utils

      Public
      Grid utilities for 2D/3D image manipulations in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•0•1•Updated Jul 11, 2025Jul 11, 2025

    • torch-fourier-shell-correlation

      Public
      Calculate the Fourier shell correlation in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•1•0•Updated Jul 10, 2025Jul 10, 2025

    • torch-transform-image

      Public
      Real space transformations of 2D/3D images in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•1•1•Updated Jul 7, 2025Jul 7, 2025

    • imodmodel

      Public
      IMOD model files as pandas dataframes in Python
      Python
      •
      Other
      •8•11•3•0•Updated Jun 26, 2025Jun 26, 2025

    • tttsa

      Public
      Automated tilt-series alignment for cryo-ET in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•7•0•Updated Jun 26, 2025Jun 26, 2025

    • torch-find-peaks

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•2•0•Updated Jun 20, 2025Jun 20, 2025

    • torch-refine-tilt-axis-angle

      Public
      Tilt-axis angle optimization for tilt series using common lines in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•0•Updated Jun 12, 2025Jun 12, 2025

    • starfile

      Public
      STAR file I/O in Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •19•51•4•1•Updated Jun 2, 2025Jun 2, 2025

    • torch-fourier-shift

      Public
      Translate 2D/3D images by phase shifting Fourier transforms in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•3•1•Updated May 30, 2025May 30, 2025

    • torch-surface-skeletonization

      Public
      skeletonize a 3D surface from a segmentation
      0•0•0•0•Updated May 29, 2025May 29, 2025

    • fidder

      Public
      Detect and erase gold fiducials in cryo-EM images
      Python
      •
      Other
      •4•15•4•1•Updated May 27, 2025May 27, 2025

    • torch-image-interpolation

      Public
      Interpolation and gridding for 2D and 3D images in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•5•0•1•Updated May 22, 2025May 22, 2025

    • torch-affine-utils

      Public
      Utilities for affine transforms of 2d/3d coordinates in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•1•0•Updated May 13, 2025May 13, 2025

    • eerfile

      Public
      Read electron event representation (EER) files in Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•7•7•0•Updated May 12, 2025May 12, 2025

    • torch-cryoeraser

      Public
      Erase regions in cryo-EM images in PyTorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Apr 29, 2025Apr 29, 2025

    • torch-so3

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•0•1•Updated Apr 23, 2025Apr 23, 2025