39 projects
teamtomo
Modular Python packages for cryo-EM and cryo-ET
torch-affine-utils
Utilities for affine transforms of 2d/3d coordinates in PyTorch
torch-motion-correction
Motion estimation and correction in PyTorch
torch-find-peaks
Peak finding and fitting using torch
torch-so3
Generate uniform 3D euler angles (ZYZ)
torch-2dtm
2D template matching in pytorch
torch-fourier-slice
Fourier slice extraction/insertion in PyTorch.
torch-tiltxcorr
Cross correlation with cosine stretching for cryo-EM data in PyTorch
torch-subpixel-crop
Extract 2D/3D subimages with subpixel precision in PyTorch
torch-grid-utils
Grid utilities for 2D/3D image manipulations in PyTorch
torch-tilt-series
Tilt series data structure, projection and subtilt extraction for cryo-ET.
torch-segment-fiducials-2d
A small pre-trained residual U-Net for gold fiducial segmentation in cryo-EM images
torch-transform-image
Real space transformations of 2D/3D images in PyTorch
torch-refine-tilt-axis-angle
Tilt-axis angle optimization for tilt series using common lines in PyTorch
torch-fourier-shift
Shift 2D/3D images by phase shifting Fourier transforms in PyTorch
torch-ctf
CTF calculation for cryoEM in torch
torch-image-interpolation
Linear interpolation and gridding for 2D and 3D images in PyTorch
torch-cryoeraser
Erase masked regions from cryo-EM images
torch-fourier-shell-correlation
Compute the Fourier shell correlation in PyTorch
torch-fourier-rescale
Rescale 2D and 3D images by Fourier padding/cropping in PyTorch
teamtomo-basemodel
Custom BaseModel class and type-hints for using Pydantic within TeamTomo.
torch-cubic-spline-grids
Cubic spline interpolation on multidimensional grids in PyTorch
etomofiles
A Python package for reading IMOD etomo alignment files into pandas DataFrames
dynamotable
Read and write Dynamo table files as pandas dataframes
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.
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
