├── .github └── workflows │ └── testing.yml ├── .gitignore ├── .gitmodules ├── CHANGELOG.rst ├── LICENSES ├── BSD-3-Clause.txt ├── CC-BY-4.0.txt ├── CC0-1.0.txt └── MIT.txt ├── README.rst ├── REUSE.toml ├── doc ├── .gitignore ├── CHANGELOG.rst ├── Makefile ├── brightness.rst ├── changepoint.rst ├── conf.py ├── enclosing_circles.svg ├── enclosing_circles.svg.license ├── flatfield.rst ├── fret.rst ├── funcs.rst ├── helper.rst ├── image.rst ├── index.rst ├── io.rst ├── loc.rst ├── make.bat ├── motion.rst ├── multicolor.rst ├── nbui.rst ├── optimize.rst ├── plot.rst ├── roi.rst ├── sim.rst ├── spatial.rst └── stats.rst ├── pyproject.toml ├── sdt ├── __init__.py ├── _version.py ├── brightness.py ├── changepoint │ ├── __init__.py │ ├── bayes_offline.py │ ├── bayes_online.py │ ├── pelt.py │ └── utils.py ├── config.py ├── exceptions.py ├── flatfield.py ├── fret │ ├── __init__.py │ ├── sm_analyzer.py │ ├── sm_plot.py │ ├── sm_track.py │ └── utils.py ├── funcs.py ├── gui │ ├── SdtGui │ │ ├── BatchWorker.qml │ │ ├── ChannelConfig.qml │ │ ├── DataCollector.qml │ │ ├── DatasetSelector.qml │ │ ├── DirSelector.qml │ │ ├── EditableComboBox.qml │ │ ├── EditableSpinBox.qml │ │ ├── FrameSelector.qml │ │ ├── Handle.qml │ │ ├── ImageDisplay.qml │ │ ├── ImageSelector.qml │ │ ├── ImageViewer.qml │ │ ├── LocOptions.qml │ │ ├── Locator.qml │ │ ├── MplPathShape.qml │ │ ├── MultiDataCollector.qml │ │ ├── ROILabel.qml │ │ ├── ROISelector.qml │ │ ├── RealSpinBox.qml │ │ ├── Registrator.qml │ │ ├── ResizeHandles.qml │ │ ├── Sdt.qml │ │ ├── StatusDisplay.qml │ │ ├── TrackOptions.qml │ │ └── qmldir │ ├── __init__.py │ ├── __main__.py │ ├── _mpl_path_elements.py │ ├── batch_worker.py │ ├── channel_config.py │ ├── data_collector.py │ ├── dataset.py │ ├── frame_selector.py │ ├── image_pipeline.py │ ├── image_viewer.py │ ├── item_models.py │ ├── legacy │ │ ├── __init__.py │ │ ├── locator │ │ │ ├── __init__.py │ │ │ ├── __main__.py │ │ │ ├── algorithms.py │ │ │ ├── app.py │ │ │ ├── batch_progress.py │ │ │ ├── batch_progress.ui │ │ │ ├── batch_progress.ui.license │ │ │ ├── file_chooser.py │ │ │ ├── file_chooser.ui │ │ │ ├── file_chooser.ui.license │ │ │ ├── file_options.ui │ │ │ ├── file_options.ui.license │ │ │ ├── locate_filter.py │ │ │ ├── locate_filter.ui │ │ │ ├── locate_filter.ui.license │ │ │ ├── locate_options.py │ │ │ ├── locate_options.ui │ │ │ ├── locate_options.ui.license │ │ │ ├── locate_saver.py │ │ │ ├── locate_saver.ui │ │ │ ├── locate_saver.ui.license │ │ │ ├── main_window.py │ │ │ ├── t2d_options.ui │ │ │ ├── t2d_options.ui.license │ │ │ ├── trackpy_options.ui │ │ │ ├── trackpy_options.ui.license │ │ │ └── workers.py │ │ ├── option_model.py │ │ └── widgets │ │ │ ├── __init__.py │ │ │ ├── micro_view.py │ │ │ ├── micro_view_widget.ui │ │ │ └── micro_view_widget.ui.license │ ├── loc_display.py │ ├── loc_options.py │ ├── locator.py │ ├── mpl_backend.py │ ├── option_chooser.py │ ├── process_worker.py │ ├── py_image.py │ ├── qml_wrapper.py │ ├── registrator.py │ ├── roi_selector.py │ ├── sdt.py │ ├── thread_worker.py │ ├── track_display.py │ └── track_options.py ├── helper │ ├── __init__.py │ ├── numba.py │ ├── pandas.py │ ├── raise_in_thread.py │ ├── singleton.py │ └── slicerator.py ├── image │ ├── __init__.py │ ├── filters.py │ ├── masks.py │ ├── threshold.py │ └── utils.py ├── io │ ├── __init__.py │ ├── fs.py │ ├── image_sequence.py │ ├── sm.py │ ├── tiff.py │ └── yaml.py ├── loc │ ├── __init__.py │ ├── bg_estimator.py │ ├── cg │ │ ├── __init__.py │ │ ├── algorithm.py │ │ ├── api.py │ │ ├── find.py │ │ └── restrict_roi.py │ ├── daostorm_3d │ │ ├── __init__.py │ │ ├── algorithm.py │ │ ├── api.py │ │ ├── data.py │ │ ├── find.py │ │ ├── find_numba.py │ │ ├── fit.py │ │ ├── fit_impl.py │ │ ├── fit_numba.py │ │ └── fit_numba_impl.py │ ├── make_batch.py │ ├── raw_features.py │ ├── restrict_roi.py │ ├── snr_filters.py │ └── z_fit.py ├── motion │ ├── __init__.py │ ├── immobilization.py │ ├── msd.py │ ├── msd_base.py │ └── msd_dist.py ├── multicolor │ ├── __init__.py │ ├── coloc.py │ ├── frame_selector.py │ └── registrator.py ├── nbui │ ├── __init__.py │ ├── channel_splitter.py │ ├── file_dialog.py │ ├── image_display.py │ ├── image_selector.py │ ├── locator.py │ ├── roi_selector.py │ └── thresholder.py ├── optimize │ ├── __init__.py │ ├── affine_fit.py │ ├── exp_fit.py │ ├── gaussian_fit.py │ └── ransac.py ├── plot.py ├── roi │ ├── __init__.py │ ├── imagej.py │ ├── mask_roi.py │ └── roi.py ├── sim │ ├── __init__.py │ ├── fluo_image.py │ └── sm_tracks.py ├── spatial.py ├── stats.py └── testing.py └── tests ├── __init__.py ├── conda-env.yml ├── daostorm_3d ├── __init__.py ├── data_algorithm │ ├── beads_2d.npz │ ├── beads_2d.npz.license │ ├── beads_2dfixed.npz │ ├── beads_2dfixed.npz.license │ ├── beads_3d.npz │ └── beads_3d.npz.license ├── data_find │ ├── bead_finder.npz │ ├── bead_finder.npz.license │ ├── bead_img.npz │ └── bead_img.npz.license ├── data_fit │ ├── beads_fit_2d.npz │ ├── beads_fit_2d.npz.license │ ├── beads_fit_2dfixed.npz │ ├── beads_fit_2dfixed.npz.license │ ├── beads_fit_3d.npz │ ├── beads_fit_3d.npz.license │ ├── beads_iter_2d.npz │ ├── beads_iter_2d.npz.license │ ├── beads_iter_2dfixed.npz │ ├── beads_iter_2dfixed.npz.license │ ├── beads_iter_3d.npz │ ├── beads_iter_3d.npz.license │ ├── calc_peaks.npy │ ├── calc_peaks.npy.license │ ├── fit_img.npz │ ├── fit_img.npz.license │ ├── fit_img_with_bg.npy │ ├── fit_img_with_bg.npy.license │ ├── iterate_2d_fixed.npy │ ├── iterate_2d_fixed.npy.license │ ├── z_params.yaml │ ├── z_sim_finder.npz │ ├── z_sim_finder.npz.license │ ├── z_sim_fit_z.npz │ ├── z_sim_fit_z.npz.license │ ├── z_sim_img.npz │ ├── z_sim_img.npz.license │ ├── z_sim_iter_z.npz │ └── z_sim_iter_z.npz.license ├── test_algorithm.py ├── test_api.py ├── test_data.py ├── test_find.py ├── test_find_numba.py ├── test_fit.py └── test_fit_numba.py ├── data_changepoint ├── offline_full_multiv.npz ├── offline_full_multiv.npz.license ├── offline_gauss_univ.npz ├── offline_gauss_univ.npz.license ├── online.npz └── online.npz.license ├── data_exp ├── ode_solve.npy ├── ode_solve.npy.license ├── ode_tangent.npy └── ode_tangent.npy.license ├── data_image ├── cg.npz ├── cg.npz.license ├── wavelet_bg.npz └── wavelet_bg.npz.license ├── data_io ├── ij.tif ├── ij.tif.license ├── msdplot.h5 ├── msdplot.h5.license ├── orig_pkc.h5 ├── orig_pkc.h5.license ├── orig_pks.h5 ├── orig_pks.h5.license ├── orig_pt2d.h5 ├── orig_pt2d.h5.license ├── orig_thunderstorm.h5 ├── orig_thunderstorm.h5.license ├── orig_trc.h5 ├── orig_trc.h5.license ├── pMHC_AF647_200k_000_.pkc ├── pMHC_AF647_200k_000_.pkc.license ├── pMHC_AF647_200k_000_.pks ├── pMHC_AF647_200k_000_.pks.license ├── pMHC_AF647_200k_000__ch1.mat ├── pMHC_AF647_200k_000__ch1.mat.license ├── pMHC_AF647_200k_000__ch1.txt ├── pMHC_AF647_200k_000__ch1.txt.license ├── pMHC_AF647_200k_000__positions.mat ├── pMHC_AF647_200k_000__positions.mat.license ├── pMHC_AF647_200k_000__protocol.mat ├── pMHC_AF647_200k_000__protocol.mat.license ├── pMHC_AF647_200k_000__tracks.mat ├── pMHC_AF647_200k_000__tracks.mat.license ├── pMHC_AF647_200k_000__tracks.trc ├── pMHC_AF647_200k_000__tracks.trc.license ├── test_000_.SPE ├── test_000_.SPE.license ├── thunderstorm.csv └── thunderstorm.csv.license ├── data_loc ├── cg_loc_orig.npz ├── cg_loc_orig.npz.license ├── cg_local_max_orig.npz ├── cg_local_max_orig.npz.license ├── pMHC_AF647_200k_000_.npz ├── pMHC_AF647_200k_000_.npz.license └── params.yaml ├── data_motion ├── 00_index.txt ├── 00_index.txt.license ├── B-1_000__positions.mat ├── B-1_000__positions.mat.license ├── B-1_000__protocol.mat ├── B-1_000__protocol.mat.license ├── B-1_000__tracks.mat ├── B-1_000__tracks.mat.license ├── B-1_000__tracks.trc ├── B-1_000__tracks.trc.license ├── B-1_001__positions.mat ├── B-1_001__positions.mat.license ├── B-1_001__protocol.mat ├── B-1_001__protocol.mat.license ├── B-1_001__tracks.mat ├── B-1_001__tracks.mat.license ├── B-1_001__tracks.trc ├── B-1_001__tracks.trc.license ├── all_displacements.pkl ├── all_displacements.pkl.license ├── all_sd_cdf.pkl ├── all_sd_cdf.pkl.license ├── all_square_displacements.pkl ├── all_square_displacements.pkl.license ├── bla_ch1.mat ├── bla_ch1.mat.license ├── displacements_B-1_000_.npy ├── displacements_B-1_000_.npy.license ├── emsd.h5 ├── emsd.h5.license ├── emsd_matlab.npy ├── emsd_matlab.npy.license ├── imsd.h5 ├── imsd.h5.license ├── msd.h5 ├── msd.h5.license ├── square_displacements.npy └── square_displacements.npy.license ├── data_roi ├── ellipse.roi ├── ellipse.roi.license ├── ellipse_roi.npz ├── ellipse_roi.npz.license ├── freehand.roi ├── freehand.roi.license ├── oval.roi ├── oval.roi.license ├── polygon.roi ├── polygon.roi.license ├── rect.roi ├── rect.roi.license ├── rects.zip ├── rects.zip.license ├── traced.roi └── traced.roi.license ├── data_sim ├── gaussians.npz └── gaussians.npz.license ├── test_brightness.py ├── test_changepoint.py ├── test_config.py ├── test_flatfield.py ├── test_fret.py ├── test_funcs.py ├── test_gui ├── __init__.py ├── conftest.py ├── test_dataset.py ├── test_frame_selector.py ├── test_image_display.py ├── test_image_selector.py ├── test_image_viewer.py ├── test_item_models.py ├── test_mpl_path_elements.py ├── test_option_chooser.py ├── test_py_image.py ├── test_qml_wrapper.py ├── test_roi_selector.py ├── test_sdt.py ├── test_thread_worker.py └── utils.py ├── test_helper.py ├── test_image.py ├── test_io.py ├── test_loc.py ├── test_loc_cg.py ├── test_motion.py ├── test_multicolor.py ├── test_multicolor_registrator.py ├── test_optimize_affine_fit.py ├── test_optimize_exp_fit.py ├── test_optimize_gaussian_fit.py ├── test_optimize_ransac.py ├── test_roi.py ├── test_sim.py ├── test_slicerator.py ├── test_spatial.py ├── test_stats.py └── test_testing.py /.github/workflows/testing.yml: -------------------------------------------------------------------------------- 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