Bruker Python Packages

pyspm

Python library to handle Scanning Probe Microscopy Images. Can read nanoscan .xml data, Bruker AFM images, Nanonis SXM files as well as iontof images(ITA, ITM and ITS).

brukeropus

A python package for communicating with Bruker OPUS spectroscopy software and reading its binary file format.

thyra

A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.

opentimstdf

Pure-Rust reader for Bruker timsTOF .tdf / .tdf_bin files, with Python bindings.

finalcif

A CIF file finalizer for small molecule crystallography with as much automation as possible.

brukeropusreader

Python package for reading Bruker OPUS files.

tdfpy

Python package for parsing Bruker timsTOF data (PRM, DDA, DIA) + 3d centroiding & noise filtering

bafpipe

Automated deconvolution of Bruker mass spectra datasets using UniDec

epyr-tools

Professional Python toolkit for EPR spectroscopy data analysis. Load Bruker files, apply baseline correction, analyze lineshapes, and convert to FAIR formats. Complete CLI suite with comprehensive testing.

alphaviz

AlphaViz is a cutting-edge browser-based interactive visualization tool allowing to visualize the processed mass spectrometry data acquired with Bruker instrument.

bruker

A modular toolkit for Bruker MRI raw-data handling.

deconvolawrence

Automated deconvolution of Bruker mass spectra datasets using UniDec

tdfextractor

Extract MS2, MGF, and mzML files from Bruker timsTOF .d folders

spxtacular

spxtacular is a Python library for mass spectrometry spectrum processing. It provides a chainable Spectrum API covering the full centroid-to-neutral-mass pipeline: denoising, isotope deconvolution, neutral mass conversion, fragment matching, and PSM scoring.

pysspfm

PySSPFM: A specialized tool for Switching Spectroscopy Piezoresponse Force Microscopy (SSPFM) data processing

opentdf

Rust reader for timsTOF .d/ (TDF) mass spectrometry bundles