A curated list of repositories, tools, and projects maintained by the BAMresearch organization researchers. The repositories are listed according to the overarching topic and sorted with respect to their field of application. This list is updated once every month to record new developments at BAM.

• image_processing_ioc – IOC that takes one or two files and exposes image analysis results.
• Roughness-Analysis-by-Electron-Microscopy – Roughness analysis approach by electron microscopy for spherical microparticles.
• DF-TEM-PAW – This repository contains the necessary sources and scripts to conduct automated precipitate analysis as demonstrated in [10.1007/s40192-023-00331-5]
• PassiveSmartDust – An adjustable image segmentation filter, combined with data procession used in the PSD project.

• HavNegpy – HavNegpy is a python fit package to anaylze dielectric spectroscopy data. HavNeg is an acronym for Havriliak and Negami function, and the fit module is written specifically to analyze the dielectric loss and real part of AC conductivity data.
• PepGM - A probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores.
• TGA-FTIR-hyphenation-tool-kit – Analysis of hyphenated TGA and FTIR data in Jupyter Notebooks: quantitative evolved gases analysis, release rate deconvolution, easy to adapt for different devices.
• virtual-gas-camera – Software repository for the so-called 'virtual gas camera' associated with the paper 'Robotic Scanning Absorption Spectroscopy for Methane Leak Detection: the Virtual Gas Camera'.

• bayem – Implementation and derivation of "Variational Bayesian inference for a nonlinear forward model." [Chappell et al. 2008] for arbitrary, user-defined model errors.
• probeye – A general framework for setting up parameter estimation problems.
• b-least-analysis – Calibration tool for measurement data with ISO 6143-based model fitting and uncertainty estimation.

• pymatgen – Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. It powers the Materials Project.
• ZrV2O7-PDF-Refinement - Python scripts specifically developed for structural refinement of Zirconium Vanadate (ZrV₂O₇).

• LobsterPy – Package to automatically analyze Lobster runs.
• lobster-database-paper-analysis-scripts – Repository Consisting of analysis scripts.

• jupyter-analysis-tools – Common Python helpers for data analysis notebooks in GIT repositories.
• WavenumberAnalysis – This project allows to perform wavenumber mapping using Matlab.

• bam-masterdata – Repository containing the masterdata definitions of the BAM Data Store project.
• dalapp – Datastore Advanced Label App.
• dataMerge – A tool for merging and/or rebinning data to achieve a lower point density with best possible statistics.
• datastore-generic-uploader – A Data Store upload helper with flexible choice of object types and their parents/children dependencies. Based on Bastian Rühles Code.
• datastoredays25-group2 – A repository containing the documentation of the Group 2 for the Data Store Days organized in BAM on 9-11 April 2025.
• dcu – Data Collection Utility.
• pybis_workshop – This is the material for the pyBIS-Workshops of the project BAM Data Store.
• ExtPybis - ExtPybis is an extension of the Pybis library meant for improving data synchronisation with an openBIS datastore.
• masterdata-checker – Python package used to check the correctness of a given Masterdata definitions file with respect to the entities already registered in the BAM Data Store.
• masterdata-generator – A minimal cookiecutter template to generate repositories for BAM Masterdata definitions.
• masterdata-template – A template to create and work with data models in the BAM Data Store
• masterdata_test – Repository for the webinar IV, phase IV.
• openbis-upload-helper – Upload Helper Tool and Parsers for OpenBIS in the BAM Data Store.
• openBIS2SQLite

• NFDI4IngHPCWorkflows – In this repository, we would like to investigate how (docker, apptainer) containers can be build in order to improve the FAIRness of workflows in the HPC context.
• NFDI4IngModelValidationPlatform – A collection of benchmarks and methdology for provenance tracking for the validation of simulation models.
• NFDI4IngScientificWorkflowRequirements – This is a repository to discuss, collect and store the requirements for scientific workflow systems

• automatic-sem-image-segmentation – Workflow for Simulation and Automatic Semantic Segmentation of Electron Microscopy Images.
• Photothermal_SR_Net - Model to reconstruct a defect pattern with IR cameras.
• SRGDM – Super-Resolution for Gas Distribution Mapping.

• EISnet - Code for model to Machine Learning-Assisted Equivalent Circuit Identification for Dielectric Spectroscopy of Polymers https://doi.org/10.1016/j.electacta.2024.144474.
• ANNforPAT – This code accompanies the paper "Artificial neural networks for quantitative online NMR spectroscopy" (https://doi.org/10.1007/s00216-020-02687-5)
• fiora - An in silico fragmentation algorithm designed to predict tandem mass spectra (MS/MS) with high accuracy. Using graph neural networks, FIORA models bond cleavages, fragment intensities, and estimates retention times (RT) and collision cross sections (CCS).

• equitrain - Equitrain is an open-source software package designed to simplify the training and fine-tuning of machine learning universal interatomic potentials (MLIPs).
• autoplex – Software for generating and benchmarking machine learning (ML) based interatomic potentials.
• SynCoTrainMP - Co-Training for Crystal Synthesizability Prediction.

• chatBIS – A conversational AI assistant for the openBIS research data management system. Uses RAG with Ollama to provide natural, accurate responses to queries about openBIS. Scrapes documentation, processes it into semantic chunks, and delivers helpful answers through a simple command-line interface.

• fenics-constitutive – Complex constitutive models beyond the FEniCS UFL.
• fenics-reinforcement -
• fenics_helpers – Little Helper classes that come up repeatedly when writing solvers in FEniCS.
• FenicsConcrete – FE (Finite Element) model representing the hardening of concrete.
• FenicsXConcrete - FE (Finite Element) model representing the hardening of concrete.
• FEniQS – A library for modelling static/quasi-static structural mechanics problems in FEniCS.
• VMAP4Fenics – VMAP Wrapper for Fenics FEM Simulations.
• xdmfConverter – convert xdmf file written by dolfin including multiple attributes over time to a xdmf file summarizing all attributes for one time step together allowing additional filter functions from paraview.
• PGDrome – A FEniCS based python module of the Proper Generalized Decomposition (PGD) method.

• McDLS – Employs a Monte Carlo method to derive size distributions from dynamic light scattering (DLS) data. Based on https://github.com/BAMresearch/McSAS.
• particle_concentration_from_dls – A python implementation for determining nanoparticle number concentrations from multi-angle dynamic light scattering (DLS) measurements. Based on https://doi.org/10.1007/s11051-020-04840-8(https://doi.org/10.1007/s11051-020-04840-8).
• analyse_dls_with_contin – This repository contains Python code and a Jupyter Notebook running the original CONTIN program by S. Provencher on every DLS measurement (dynamic light scattering, aka. photon correlation spectroscopy, PCS) read from *.ASC files.
• McSAS – A tool for extracting form-free size distributions of small-angle scattering (SAS) patterns using a Monte-Carlo method.
• McSAS3 – Refactored McSAS for analysis of X-ray and neutron scattering data.
• McSAS3GUI - Graphical User Interface for McSAS3
• SasModelsExplorer - A PyQt-based interactive application to explore scattering models
• jupyter_tutorial_sas – A programming tutorial for looking at SAS Data with Python. Part of the 'Better with Scattering' Workshop.
• Overview-of-SAXSess-Measurements – Jupyter Notebooks for giving an overview or generating overview plots.
• Utah-SAXS-Tools – The Utah SAXS Tools (USToo), adapted for Python 3, originally by David P. Goldenberg, 2009-2012
• logbook2mouse - This library reads a measurement logbook and associated project/sample information and generates a script for a SAXS instrument. Currently still under development.
• MOUSEDataPipeline – Tools for (automatic) processing of the new MOUSE datafiles
• SPONGE – Simulates X-ray and Neutron scattering patterns from arbitrary shapes defined by STL files
• UltimaRatio – A high resolution 3D FFT package (primarily for X-ray scattering simulation).
• MoDaCor – new modular data corrections for any neutron or xray technique that produces 1D or 2D scattering/diffraction/imaging data.

• nBio_docs – TOPAS-nBio Documentation
• TOPAS-CellModels – Cell Models for TOPAS/Geant4 and the inclusion of nano particles in particle scattering simulations. The C++ classes in this repository extend the functionality of the TOPAS (http://www.topasmc.org/) MC program, which is itself a wrapper of the Geant4 MCS Toolkit (http://geant4.org).
• TOPAS-nBio – TOPAS-nBio extension repository, for documentation and license see: https://topas-nbio.readthedocs.io/

• aRTist-handbook – User guide for the radiographic simulator aRTist.
• aRTist-PythonLib – Python library to control aRTist remotely and automatically
• ctsimu-artist-module – CTSimU Module for aRTist
• ctsimu-scenarios – A file format to describe CT scans.
• ctsimu-toolbox – CTSimU Software Toolbox

• parallel-abus – This code is a Python implementation of the parallelized adaptive Bayesian Updating with Structural reliabilty methods.
• PyParSeis - Python code for Parallel Seismic test valuation (determination of foundation depth).
• ScaffoldStructures – Create different scaffolds based on triply periodic minimal structures like Gyroids or SchwarzP cells.

• gaden2 – GADEN: A 3D Gas Dispersion Simulator for Mobile Robot Olfaction in Realistic Environments.

• NibelungenbrueckeDemonstrator – Provides a representative and repeatable workflow for the implementation of a stochastic Digital Twin (DT) of the Nibelungenbrücke in Worms (Germany).

• SyFoS – Synthetic Force Spectroscopy data - A graphical user interface.
• SOFA – SOftware for Force Analysis - A graphical user interface to analyze Atomic Force Microscopy Force Spectroscopy data.

• SequentialLearningApp – Sequential Learning App for Materials Discovery (SLAMD)
• WEBSLAMD – Sequential Learning App for Materials Discovery ("SLAMD") - Web Version
• SLAMD_Doku

• EPICS-synApps-assemble – synApps assemble script.
• epics_dashboard – Streamlit based dashboard to display EPICS process variables in real time.
• NetworkedPortentaIOC – EPICS IOC for addressing the networked portenta. Simple, functional version for starters.
• harvard_phd_ioc – EPICS IOC for the Harvard PhD syringe pump connected via a network-to-serial converter.
• spec2epics – Scripts to convert the configuration of IMS/Schneider MDrive motors from SPEC to EPICS motorIMS.
• Trinamic_TMCL_IOC – A python and EPICS interface for Trinamic TMCL-speaking motor controller boards, controlled over serial-over-ethernet.
• pressure_gauge_ioc - EPICS IOC for reading pressure from Inficon pressure gauge.

• Ontopanel-backend – Diagrams.net plugin for ontology development.
• Ontopanel-BrinellHardnessData – File archive of Brinell hardness testing.
• Ontopanel-frontend – Frontend of Ontopanel application.

• Micro_plastic_relationship_counseling – Server-Client socket implementation that allows for log file based error detection and termination of a program with a GUI.
• IOCLauncher - A simple dashboard to launch and keep track of command-line-launched services
• apm_planner – APM Planner Ground Control Station (Qt).

• Advanced_Jobflow_Tutorial – This is a repository containing an advanced tutorial for jobflow (https://github.com/materialsproject/jobflow) related to computational materials science.
• atomate2 – atomate2 is a library of computational materials science workflows.

• amworkflow - Module for creating automated workflows in the context of concrete additive manufacturing.

• Fire_Propagation – Code base for the creation of a fire propagation dataset by combining burned area shapefiles and active fire detections.
• wildfire_prop_database – Example for merging swath paths into a single scene and extracting a burned area polygon from the resulting image.

• LiveFT – An educational tool showing in realtime the webcam image and the intensity of its Fourier Transform next to it.
• pipeline-webxr - A Next.js application for visualizing 3D models in augmented reality using Babylon.js.
• EU-energy-label-app - Flutter based app project for finding energy and environmental information on products carrying the new European energy label. This repo provides a quick start for mobile app development and consists of a fully functional app for iOS and Android which can be tailored to your needs.

• Regression-Analysis-for-Materials-Sciences---RAMSES – An Application for Concrete Strength Prediction.

• ABID - R code to locally run an R Shiny-App described in "Tscheuschner et al. (2022) Methods for antibody identification in one hour – examined with murine anti-SARS-CoV-2 Mabs".
• BallTracker – Tracks a ball to calibrate an axis. For parallel beam geometries.
• DIRECTT – A graphical user interface, based on the ASTRA toolbox, for the reconstruction from X-ray Computed Tomography data. It includes the option of the DIRECTT algorithm.

• 2PP-TestArtifact – Contains a 2PP-test artifact.
• CookieCutters – 3D-printable elements Cookie Cutters we created for the international year of the Periodic Table 2019.
• ElectricSafetyInterlock – Schematics, pictures, parts list and documents for an electric safety interlock (ESI).
• OOMMF-temperature – Provides input parameter files (MIF) to include temperature in micromagnetc simulations with the Object Oriented Micromagnetic Framework (OOMMF).
• PluripotentTemperatureController – Electrical diagram, parts list and photos for building a triple PID controller with AC and DC solid-state relays.
• MultilayerInternalStresses - Effect of reaction layers on internal stresses in co-fired multilayers of calcium manganate and calcium cobaltite.
• Round-Robin-Hybrid-Mixtures - Associated to World's first round robin test on hybrid mixtures: https://doi.org/10.1016/j.jlp.2022.104947.

• MALDI-TOF-database – This project contains a database which classifies polymer structures according to their repeat unit masses, as obtained by MALDI ToF measurements.

• MAPz_at_BAM – Materials Acceleration Platform Center at BAM

• dectris_eiger_ioc – A simple caproto-based IOC for setting, triggering and collecting data to files from the Dectris Eiger detectors.
• Lauda_Proline_IOC – A Caproto IOC for basic control of the Lauda Proline RP855C bath.

• pyscicat - Pyscicat is a python client library for interacting with the SciCat backend.
• SciCat-localdeploy – SciCat Data Catalog Kubernetes Deployment - Install scripts setting up SciCat on a single server using minikube or in baremetal k8s cluster.
• scicat-upload – scicat ingestion/upload scripting for uploading meta data into the database.

• yapy-cookiecutter – Yet Another cookiecutter template for Python projects in data science & processing.
• yapy-copier-template – Yet Another Python Copier template for a Python modules and applications focussing on data science, processing and analysis.

• rl_logging – RobotLibraries Logging Abstraction
• ros2_tools – Tools for the Robot Operating System 2 (ROS 2)

• bam-load-based-testing - Two-mass building model for load-based testing of heat pumps. The model is used to define the inertial behavior of the heat sink.
• BeamlineAutomationRS232 - A collection of Python drivers for RS-232 control of common beamline components at the mySpot beamline of BESSY-II.
• checksum-dir – simple script for creating and verifying file checksums for a directory recursively.
• dockerbuilder-pmd – Repo for building docker images in github actions.
• GaussianBeamProfile – Gaussian Beam Profile calculator for 2PP.
• HDF5Translator – A flexible command-line tool for translating HDF5 files with one structure into HDF5 files with another structure using editable configuration dictionaries.
• jetlog – Jetlog - JSON-based extendible logging.
• jupyter-integration – Configures Anaconda on Windows and associates double-click on .ipynb files with JupyterLab. To get version controlled Jupyter notebooks, it installs an extension to commit changes directly from JupyterLab, no command-line interaction necessary. https://bamresearch.github.io/jupyter-integration
• LebeDigital – The LeBeDigital Concrete Production and Testing Ontology - CPTO Repository.
• Mistle - Mistle is a fast spectral search engine. It uses a fragment-indexing technique and SIMD intrinsics to match experimental MS2 spectra to large spectral libraries at a high performance. https://doi.org/10.1093/bioinformatics/btad376
• NetworkedPortenta – Arduino IDE code to expose the I/O of an Arduino Portenta Machine Control to an ethernet network.
• nomad-parser-fireworks – A NOMAD parser plugin for the FireWorks output JSON file.
• PrusaSlicer – G-code generator for 3D printers (RepRap, Makerbot, Ultimaker etc.).
• pyrxiv – A Python package for retrieving arXiv papers and filter them out with respect to some specific regex pattern.
• pytest-notebook – A pytest plugin for regression testing and regenerating Jupyter Notebooks.
• Reproducible-Science – Provide ideas, instructions and templates on how to realize reproducible science. https://bamresearch.github.io/Reproducible-Science/.
• tiled – API to structured data.

This list is licensed under the Creative Commons Attribution 4.0 International license.