Cryo Em Python Packages

cryosparc-tools

Python library that enables scripting access to CryoSPARC, a cryo-EM software package.

cctbx-base

Computational Crystallography Toolbox

powerfit-em

Rigid body fitting of atomic strucures in cryo-electron microscopy density maps

vitrio

High throughput Cryo-EM image I/O library for Python

leopard-em

Two-Dimensional Template Matching implemented in Python

topaz-em

Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.

mdcatch

Fetch metadata from EPU / SerialEM and launch on-the-fly pre-processing

superpose3d

register 3D point clouds using rotation, translation, and scale transformations.

cctbx

Computational Crystallography Toolbox

himena-relion

A modern RELION GUI

helicon

Tools for cryo-EM analysis of helical structures

biomcp-server

🧬 BioMCP — bioinformatics MCP server: 83 tools · 43 databases · PubMed/NCBI/BLAST/PDB/UniProt/enrichment · `pip install biomcp-server` · 生信 MCP 服务器

tomotwin-cryoet

cryo-ET particle picking by representation and metric learning

wwpdb-validation

Read wwPDB validation reports completely and correctly. All 36 per-residue and ~90 entry-level fields, plus the four traps that silently corrupt results.

scigantic-cryoet

Search the CZ CryoET Data Portal from Python -- a catalog and search layer over ~370 public cryo-electron tomography datasets

scigantic-emdb

Search every structure in EMDB from Python — 60,895 cryo-EM maps by protein, organism, resolution, molecular weight and PDB cross-reference.

scigantic-empiar

Explore the EMPIAR cryo-EM archive from Python — stream any of ~3,000 datasets (8.9 PiB) over parallel HTTP range reads, nothing downloaded.

scigantic-headers

Decode scientific file headers (cryo-EM, imaging, tabular, flow cytometry, mass spec, sequencing, structural biology) into typed fields. Pure, zero-dependency, with bounded parallel readers.

focustools

Python utilities for the FOCUS package

emap2lig

Official Emap2lig inference pipeline for finding ligand density blobs and building atomic ligand structures in cryo-EM maps.

cryoblob

JAX based, JIT compiled feature finding tool for low SNR cryo-EM images

cryocofi

CarbOn FIlm detector for cryo-EM images

diff-em

Differentiable Cryo-EM map fitting in JAX

imod2relion

A tool reading IMOD points, obtaining particles' info and generating .star file for RELION