39 projects
torch-tiltxcorr
Cross correlation with cosine stretching for cryo-EM data in PyTorch
torch-tilt-series
Tomogram reconstruction, subtomogram reconstruction, and subtilt extraction for cryo-ET.
torch-cubic-spline-grids
Cubic spline interpolation on multidimensional grids in PyTorch
torch-transform-image
Real space transformations of 2D/3D images in PyTorch
torch-segment-fiducials-2d
A small pre-trained residual U-Net for gold fiducial segmentation in cryo-EM images
torch-grid-utils
Grid utilities for 2D/3D image manipulations in PyTorch
torch-fourier-slice
Fourier slice extraction/insertion in PyTorch.
torch-motion-correction
Motion estimation and correction in PyTorch
torch-find-peaks
Peak finding and fitting using torch
torch-refine-tilt-axis-angle
Tilt-axis angle optimization for tilt series using common lines in PyTorch
torch-subpixel-crop
Extract 2D/3D subimages with subpixel precision in PyTorch
torch-so3
Generate uniform 3D euler angles (ZYZ)
torch-image-interpolation
Linear interpolation and gridding for 2D and 3D images in PyTorch
torch-fourier-shell-correlation
Compute the Fourier shell correlation in PyTorch
torch-fourier-shift
Shift 2D/3D images by phase shifting Fourier transforms in PyTorch
torch-fourier-rescale
Rescale 2D and 3D images by Fourier padding/cropping in PyTorch
torch-ctf
CTF calculation for cryoEM in torch
torch-2dtm
2D template matching in pytorch
torch-cryoeraser
Erase masked regions from cryo-EM images
torch-affine-utils
Utilities for affine transforms of 2d/3d coordinates in PyTorch
teamtomo-basemodel
Custom BaseModel class and type-hints for using Pydantic within TeamTomo.
dynamotable
Read and write Dynamo table files as pandas dataframes
teamtomo
Modular Python packages for cryo-EM and cryo-ET
mdocfile
SerialEM mdoc files as pandas dataframes.
mmdf
macromolecular structures (.pdb/.mmCIF) as pandas dataframes
eerfile
Read electron event representation (EER) files in Python
membrain-seg
membrane segmentation in 3D for cryo-ET
alnfile
A Python package for reading AreTomo alignment files into pandas DataFrames.
etomofiles
A Python package for reading IMOD etomo alignment files into pandas DataFrames
torch-tomogram
Tomogram reconstruction, subtomogram reconstruction, and subtilt extraction for cryo-ET.
starfile
STAR file I/O in Python
imodmodel
IMOD model files as pandas DataFrames in Python.
ttmask
CLI tool for mask creation in cryo-EM/ET
torch-image-lerp
Linear interpolation and gridding for 2D and 3D images in PyTorch
yet-another-imod-wrapper
A simple API for automated tilt-series alignment using IMOD
lil-aretomo
AreTomo (w)rapper for rln4
cryohub
IO hub for Cryo-EM, Cryo-ET and subtomogram averaging data.
cryotypes
Generalized python types and validators for cryoEM data.
fidder
U-Net for 2D fiducial segmentation in cryo-EM
