Bruker Python Packages

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.

brukeropus

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

tdfpy

Python reader for Bruker timsTOF (.d) data: DDA/DIA/PRM, fast centroiding and noise filtering

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).

finalcif

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

brukeropusreader

Python package for reading Bruker OPUS files.

spxtacular

Chainable Spectrum API for MS processing: denoising, isotope deconvolution, matching, scoring, plotting

opentimstdf

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

tdfextractor

Extract MS/MS spectra from Bruker timsTOF .d folders and convert them to MS2, MGF, or mzML.

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

opentdf

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

bafpipe

Automated deconvolution of Bruker mass spectra datasets using UniDec

pysspfm

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