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@Fluorescence-Tools fluorescence tools

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    40 repositories

    • mmfdb

      Public
      Multimodal fluorescence metadata and provenance database with a content-addressed object store and an mmCIF-derived schema.
      Python
      •
      MIT License
      •1•0•0•0•Updated Oct 26, 2026Oct 26, 2026

    • chisurf

      Public
      Global analysis platform for fluorescence data
      correlationproteinfluorescence
      correlationproteinfluorescencespectroscopymultiple-datasetsfluorescence-dataglobal-analysisfluorescence-decays-analysis
      Python
      •
      GNU General Public License v2.0
      •3•12•12•0•Updated Oct 22, 2026Oct 22, 2026

    • tttrlib

      Public
      File format agnostic low level, high performance API to read and process time-tagged-time resolved (TTTR) data for single-molecule and image spectroscopy)
      pythonsingle-moleculefluorescence
      pythonsingle-moleculefluorescenceimagingfluorescence-microscopy-imagingptuflimbeckerfluorescence-correlationpicoquant
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •4•23•1•0•Updated Sep 16, 2026Sep 16, 2026

    • IMP.bff

      Public
      IMP's Bayesian Fluorescence Framework
      spectroscopyintegrative-modeling
      spectroscopyintegrative-modeling
      C++
      •
      GNU Lesser General Public License v2.1
      •2•1•0•1•Updated Sep 13, 2026Sep 13, 2026

    • quest

      Public
      QuEst - Quenching Estimator for fluorophores coupled to proteins - active development on gitlab.peulen.xyz
      simulationfluorescencefret
      simulationfluorescencefretquenchingdyes
      Jupyter Notebook
      •
      MIT License
      •1•0•0•2•Updated Aug 11, 2026Aug 11, 2026

    • ndxplorer

      Public
      Histograms of multidimensional data
      Python
      •
      GNU General Public License v2.0
      •1•0•0•0•Updated Jun 29, 2026Jun 29, 2026

    • LabelLib

      Public
      Library for coarse-grained simulations of probes flexibly coupled to biomolecules.
      pymolfluorescencesimulation-toolkit
      pymolfluorescencesimulation-toolkitfretscience-researchaccessible-volumes
      C++
      •
      Mozilla Public License 2.0
      •2•10•0•0•Updated Apr 25, 2026Apr 25, 2026

    • fpsimp

      Public
      Fluorescent Protein Simlation Pipeline
      Python
      •
      Other
      •0•0•0•0•Updated Jan 18, 2026Jan 18, 2026

    • flr2mmcif

      Public
      Convert a spreadsheet with fluorescence information to a mmcif file for deposition in PDB-Dev
      Python
      •
      MIT License
      •1•0•0•0•Updated Jan 12, 2026Jan 12, 2026

    • clsmview

      Public
      CLSM viewer for ChiSurf
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Mar 25, 2024Mar 25, 2024

    • k2dist

      Public
      Compute and visualize orientation factor (kappa2) distributions
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Mar 25, 2024Mar 25, 2024

    • tttrconvert

      Public
      A simple converter for tttr files
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Feb 17, 2024Feb 17, 2024

    • fit2x

      Public
      Maximum likelihood fits for low photon count data - For active develeopment visit gitlab.peulen.xyz
      single-moleculefluorescencelifetime
      single-moleculefluorescencelifetimemle-estimationmleflimlifetime-analysis
      C++
      •
      Mozilla Public License 2.0
      •0•3•0•0•Updated Feb 12, 2024Feb 12, 2024

    • SAXS_score

      Public
      Python script to fit and score theoretical ensemble-averaged SAXS profile against experimental SAXS data
      Python
      •
      Mozilla Public License 2.0
      •1•1•0•0•Updated Sep 19, 2023Sep 19, 2023

    • FourierShellCorr

      Public
      Python script to compute Fourier Shell Correlation curve between two half-3D density maps
      Python
      •
      Mozilla Public License 2.0
      •1•0•0•0•Updated Sep 19, 2023Sep 19, 2023

    • distogram_MuStd

      Public
      Python script to compute and visualize residue pairwise mean distance and standard deviation of a distogram
      Python
      •
      Mozilla Public License 2.0
      •1•0•0•0•Updated Sep 19, 2023Sep 19, 2023

    • Hbond

      Public
      Python script for identifying presence of hydrogen bonds based on geometrical criteria
      Python
      •
      Mozilla Public License 2.0
      •1•0•0•0•Updated Sep 17, 2023Sep 17, 2023

    • 3D_DensityMap

      Public
      Python script to compute 3D density map for an ensemble of conformational models
      Python
      •
      Mozilla Public License 2.0
      •1•0•0•0•Updated Sep 17, 2023Sep 17, 2023

    • distogram

      Public
      Python script for calculating ensemble weighted inter-residue distance histogram (distogram)
      Python
      •
      Mozilla Public License 2.0
      •1•0•0•0•Updated Sep 15, 2023Sep 15, 2023

    • rmsd2D

      Public
      Python script for pair-wise RMSD comparison between two ensembles of protein structures
      Python
      •
      Mozilla Public License 2.0
      •1•0•0•0•Updated Sep 15, 2023Sep 15, 2023

    • RotCorrFun

      Public
      Python script to compute rotational correlation function of a protein backbone N-H vector
      Python
      •
      Mozilla Public License 2.0
      •1•0•0•0•Updated Sep 14, 2023Sep 14, 2023

    • 1D_GaussianFit

      Public
      Matlab script to fit univariate Gaussian Mixture Model (GMM) to a distribution of an observable
      MATLAB
      •
      Mozilla Public License 2.0
      •1•0•0•0•Updated Sep 14, 2023Sep 14, 2023

    • contact_map

      Public
      Python script for mapping the presence of inter-residue contacts in a biomolecule
      Python
      •
      Mozilla Public License 2.0
      •1•0•0•0•Updated Sep 14, 2023Sep 14, 2023

    • SAXS_profile

      Public
      Python script to compute theoretical ensemble-averaged SAXS profile for a biomolecule
      Python
      •
      Mozilla Public License 2.0
      •1•0•0•0•Updated Sep 14, 2023Sep 14, 2023

    • Seidel

      Public
      Seidel software for FRET-nanoscopy analysis and automated TRACE-FRET analysis
      Jupyter Notebook
      •
      Mozilla Public License 2.0
      •0•2•0•0•Updated Aug 30, 2023Aug 30, 2023

    • redRobin

      Public
      redRobin software for CELFIS analysis
      Jupyter Notebook
      •
      Mozilla Public License 2.0
      •0•1•0•0•Updated Aug 22, 2023Aug 22, 2023

    • Abberior-Tools

      Public
      python scripts for Abberior microscope
      Python
      •
      Mozilla Public License 2.0
      •0•1•0•0•Updated Sep 26, 2022Sep 26, 2022

    • avtraj

      Public
      fpssimulationfluorescence
      fpssimulationfluorescenceavsaccessible-volumesmd-trajectory
      Python
      •
      GNU Lesser General Public License v2.1
      •0•1•1•1•Updated Feb 9, 2022Feb 9, 2022

    • PAM

      Public
      This is a mirror of the PAM repository hosted on GitLab. Please refer to the GitLab repository for active development.
      MATLAB
      •
      GNU General Public License v3.0
      •1•3•1•0•Updated Aug 12, 2021Aug 12, 2021

    • FRETlines

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Aug 2, 2021Aug 2, 2021
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