.gitattributes
.gitignore
.readthedocs.yaml
Example.py
LICENSE
Make_executable.cmd
README.md
Start GUI.cmd
Start GUI.command
environment.yml
pyproject.toml
.github/workflows/publish-to-pypi.yml
.github/workflows/publish-to-testpypi.yml
docs/API reference.rst
docs/Contributing.rst
docs/GUI.rst
docs/Getting started.rst
docs/Installation.rst
docs/Makefile
docs/conf.py
docs/index.rst
docs/make.bat
docs/requirements.txt
docs/SPARXS/1_single_molecule_data_analysis.ipynb
docs/SPARXS/2_sequence_data_analysis.ipynb
docs/SPARXS/3_aligning_datasets.ipynb
docs/SPARXS/4_coupling_datasets.ipynb
docs/SPARXS/5_single_molecule_data_analysis_2.ipynb
docs/SPARXS/6_properties_per_sequence.ipynb
docs/SPARXS/global_alignment.ipynb
docs/SPARXS/index.rst
docs/_static/logo.png
docs/examples/combining_two_coordinate_sets.rst
docs/examples/copy_coordinates_between_files.rst
docs/examples/index.rst
docs/examples/merge_file_datasets.rst
docs/examples/plot_traces_overview.rst
docs/examples/save_dataset_with_selected_molecules.rst
docs/user_guide/background_subtraction.rst
docs/user_guide/channel_mapping.rst
docs/user_guide/dwell_time_analysis.rst
docs/user_guide/hidden_markov_modelling.rst
docs/user_guide/index.rst
docs/user_guide/molecule_localization.rst
docs/user_guide/trace_classification.rst
docs/user_guide/trace_extraction.rst
docs/user_guide/trace_selection.rst
docs/user_guide/trace_visualization.rst
papylio/__init__.py
papylio/__main__.py
papylio/_version.py
papylio/autoconfig.py
papylio/background_subtraction.py
papylio/coordinate_optimization.py
papylio/decorators.py
papylio/default_configuration.yml
papylio/experiment.py
papylio/file.py
papylio/file_collection.py
papylio/molecule.py
papylio/netcdf_operations.py
papylio/peak_finding.py
papylio/plotting.py
papylio/plugin_manager.py
papylio/timer.py
papylio/trace_correction.py
papylio/trace_extraction.py
papylio/trace_plot.py
papylio.egg-info/PKG-INFO
papylio.egg-info/SOURCES.txt
papylio.egg-info/dependency_links.txt
papylio.egg-info/requires.txt
papylio.egg-info/top_level.txt
papylio/analysis/2exp_fitting_SA.py
papylio/analysis/SAfitting.py
papylio/analysis/SAfitting_old.py
papylio/analysis/__init__.py
papylio/analysis/autoThreshold.py
papylio/analysis/autothreshold_batch.py
papylio/analysis/classification_simple.py
papylio/analysis/common_PDF.py
papylio/analysis/decorators.py
papylio/analysis/distributionsPanel.py
papylio/analysis/dwelltime_analysis.py
papylio/analysis/fretAnalysis.py
papylio/analysis/hidden_markov_modelling.py
papylio/analysis/interactiveAnalysis.py
papylio/analysis/plot_avgFREThist.py
papylio/analysis/stepsDataAnalysis.py
papylio/gui/main.py
papylio/gui/selection_widget.py
papylio/gui/start.py
papylio/movie/background_correction.py
papylio/movie/basic_shading_correction.py
papylio/movie/binary.py
papylio/movie/movie.py
papylio/movie/nd2.py
papylio/movie/nsk.py
papylio/movie/pma.py
papylio/movie/shading_correction.py
papylio/movie/sifx.py
papylio/movie/tif.py
papylio/plugins/__init__.py
papylio/plugins/holliday_junction/basepairing_graph.py
papylio/plugins/holliday_junction/energies.py
papylio/plugins/holliday_junction/holliday_junction.py
papylio/plugins/holliday_junction/sequence_generation.py
papylio/plugins/holliday_junction/sequence_properties.py
papylio/plugins/sequencing/Example.py
papylio/plugins/sequencing/__init__.py
papylio/plugins/sequencing/fastqAnalysis.py
papylio/plugins/sequencing/geometricHashing2.py
papylio/plugins/sequencing/geometricHashing3.py
papylio/plugins/sequencing/mapping_collection.py
papylio/plugins/sequencing/plotting.py
papylio/plugins/sequencing/sequence_generation.py
papylio/plugins/sequencing/sequence_plotting.py
papylio/plugins/sequencing/sequencing.py
papylio/plugins/sequencing/sequencing_data.py
tests/integration/test_GUI.py
tests/integration/test_file.py
tests/integration/test_file_collection.py
tests/integration/test_movie.py
tests/integration/test_netcdf_operations.py
tests/integration/test_sequence_analysis.py
tests/integration/test_sequencing_data.py
tests/integration/test_sequencing_plotting.py
tests/integration/test_sequencing_plotting_sequences.py
tests/integration/test_trace_correction.py
tests/integration/test_trace_plot.py
tests/unit/test_movie.py