lglass

openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

focustools

Python utilities for the FOCUS package

clearml

ClearML - Auto-Magical CI/CD to streamline your AI workload. Experiment Management, Data Management, Pipeline, Orchestration, Scheduling & Serving in one MLOps/LLMOps solution

espnet

End-to-End Speech Processing Toolkit

DynaMight

Tool for reconstruction and analysis of continuous heterogeneity of a cryo-EM dataset

cryodrgn

Neural networks for cryo-EM reconstruction

pdbfixer

PDBFixer fixes problems in PDB files

timm

PyTorch image models, scripts, pretrained weights -- ResNet, ResNeXT, EfficientNet, EfficientNetV2, NFNet, Vision Transformer, MixNet, MobileNet-V3/V2, RegNet, DPN, CSPNet, and more

Follow_Relion_gracefully

New script to follow Relion projects in a browser!

CryoSegNet

Customized foundational image segmentation models for picking protein particles in cryo-EM images

miffi

Cryo-EM micrograph filtering utilizing Fourier space information

ImageMagick

🧙‍♂️ ImageMagick 7

self_fourier_shell_correlation

ptolemy

Public release of Ptolemy package for automated targeting of Cryo-EM grids

examples

A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.

model-angelo

Automatic atomic model building program for cryo-EM maps

membrain-seg

membrane segmentation in 3D for cryo-ET

scipion-em-cryocare

Plugin to integrate cryoCARE: denoiser for tomography

LovelyPlots

Matplotlib style sheets to nicely format figures for scientific papers, thesis and presentations while keeping them fully editable in Adobe Illustrator.

focus

High Throughput Electron Microscopy Image Processing Software

inpainting_gmcnn

Image Inpainting via Generative Multi-column Convolutional Neural Networks, NeurIPS2018

tikz_favorites

collection of favorite TikZ graphics

pyinstrument

🚴 Call stack profiler for Python. Shows you why your code is slow!

composer

Supercharge Your Model Training

pyraug

Data Augmentation with Variational Autoencoders (TPAMI)

LearningToCountEverything

STEGO

Unsupervised Semantic Segmentation by Distilling Feature Correspondences

image-processing-tutorials

warp

pyem

Python programs for electron microscopy