├── .gitattributes ├── .gitignore ├── .hidden ├── .travis.yml ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── _config.yml ├── appveyor.yml ├── conda.recipe ├── bld.bat ├── build.sh └── meta.yaml ├── docs ├── Makefile ├── environment_py2.yml ├── environment_py35.yml ├── how_to_configure_readthedocs.txt ├── make.bat ├── rtd_requirements.txt └── source │ ├── HDF5_format.rst │ ├── HDF5_smFRET.rst │ ├── TODO.txt │ ├── absolute_beginner.rst │ ├── background.rst │ ├── burst_selection.rst │ ├── burstsearch.rst │ ├── conf.py │ ├── cython.rst │ ├── data_class.rst │ ├── dependencies.rst │ ├── exp_fitting.rst │ ├── files_description.rst │ ├── fit.rst │ ├── fret_fit.rst │ ├── fretmath.rst │ ├── gaussian_fitting.rst │ ├── getting_started.rst │ ├── index.rst │ ├── installation.rst │ ├── loader.rst │ ├── mfit.rst │ ├── notebook_workflow.rst │ ├── ph_sel.rst │ ├── phrates.rst │ ├── plots.rst │ ├── plugins.rst │ ├── readthedocs.py │ ├── reference_manual.rst │ └── releasenotes.rst ├── fretbursts ├── __init__.py ├── _version.py ├── background.py ├── bg_cache.py ├── burst_plot.py ├── burst_plot_attic.py ├── burstlib.py ├── burstlib_ext.py ├── dataload │ ├── __init__.py │ ├── manta_reader.py │ ├── multi_ch_reader.py │ ├── pytables_array_list.py │ ├── sm file structure.txt │ └── spcreader.py ├── exptools.py ├── fit │ ├── __init__.py │ ├── compare_gaussian_fit.py │ ├── compare_gaussian_fit2.py │ ├── exp_fitting.py │ ├── exp_gauss_fitting.py │ ├── fitting.py │ ├── gaussian_fitting.py │ ├── test_exp_fitting.py │ └── weighted_kde.py ├── fret_fit.py ├── fretmath.py ├── gui_selection.py ├── hdf5.py ├── legacy_mode.py ├── loader.py ├── loader_legacy.py ├── mfit.py ├── ph_sel.py ├── phtools │ ├── README.txt │ ├── __init__.py │ ├── burstsearch.py │ ├── burstsearch_c.pyx │ ├── phrates.py │ ├── phrates_cy.pyx │ ├── phrates_numba.py │ └── setup.py ├── poisson_threshold.py ├── scroll_gui.py ├── select_bursts.py ├── style.py ├── tests │ ├── __init__.py │ ├── importtest.py │ ├── nbrun.py │ ├── test_Bursts.py │ ├── test_burstlib.py │ └── test_ph_sel.py └── utils │ ├── __init__.py │ ├── examples │ ├── matplotlib_figure_mod_toolbar.py │ ├── matplotlib_fonts.py │ ├── matplotlib_gui_select.py │ ├── mpl_gui_selection.py │ ├── qt4_figure.py │ ├── timetrace_scroll_demo.py │ ├── timetrace_scroll_demo2.py │ ├── timetrace_scroll_demo3.py │ └── timetrace_scroll_pygraphqt.py │ ├── git.py │ ├── gui.py │ └── misc.py ├── notebooks ├── 1. First Steps - Start here if new to Jupyter Notebooks.ipynb ├── Example - 2CDE Method.ipynb ├── Example - Burst Variance Analysis.ipynb ├── Example - Customize the us-ALEX histogram.ipynb ├── Example - Exporting Burst Data Including Timestamps.ipynb ├── Example - FRET histogram fitting.ipynb ├── Example - Plotting timetraces with bursts.ipynb ├── Example - Selecting FRET populations.ipynb ├── Example - Working with timestamps and bursts.ipynb ├── FRETBursts - 8-spot smFRET burst analysis.ipynb ├── FRETBursts - ns-ALEX example.ipynb ├── FRETBursts - us-ALEX smFRET burst analysis.ipynb └── dev │ ├── docs │ ├── Execute notebooks.ipynb │ └── FRETBursts - Build docs.ipynb │ ├── exclude-py27.txt │ └── tests │ ├── FRETBursts - Background save and load test.ipynb │ ├── FRETBursts - Regression tests.ipynb │ ├── FRETBursts - Unit tests-debug.ipynb │ └── FRETBursts - Unit tests.ipynb ├── readthedocs.yml ├── release howto.md ├── setup.cfg ├── setup.py └── versioneer.py /.gitattributes: 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