├── .github └── workflows │ ├── build_wheels.yml │ └── sphinx.yml ├── .gitignore ├── .nojekyll ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── .nojekyll ├── Makefile ├── _templates │ └── autosummary │ │ ├── base.rst │ │ ├── class.rst │ │ └── module.rst ├── conf.py ├── img │ └── figure0_v0.png ├── index.rst ├── modules │ ├── pysted.base.Clock.reset.rst │ ├── pysted.base.Clock.rst │ ├── pysted.base.Clock.update_time.rst │ ├── pysted.base.Datamap.rst │ ├── pysted.base.Datamap.set_bleached_datamap.rst │ ├── pysted.base.Datamap.set_roi.rst │ ├── pysted.base.Detector.get_detection_psf.rst │ ├── pysted.base.Detector.get_signal.rst │ ├── pysted.base.Detector.rst │ ├── pysted.base.DonutBeam.get_intensity.rst │ ├── pysted.base.DonutBeam.rst │ ├── pysted.base.Fluorescence.get_k_bleach.rst │ ├── pysted.base.Fluorescence.get_photons.rst │ ├── pysted.base.Fluorescence.get_psf.rst │ ├── pysted.base.Fluorescence.get_sigma_abs.rst │ ├── pysted.base.Fluorescence.get_sigma_ste.rst │ ├── pysted.base.Fluorescence.rst │ ├── pysted.base.GaussianBeam.get_intensity.rst │ ├── pysted.base.GaussianBeam.rst │ ├── pysted.base.Microscope.add_to_pixel_bank.rst │ ├── pysted.base.Microscope.cache.rst │ ├── pysted.base.Microscope.clear_cache.rst │ ├── pysted.base.Microscope.empty_pixel_bank.rst │ ├── pysted.base.Microscope.get_effective.rst │ ├── pysted.base.Microscope.get_signal_and_bleach.rst │ ├── pysted.base.Microscope.is_cached.rst │ ├── pysted.base.Microscope.rst │ ├── pysted.base.Microscope.take_from_pixel_bank.rst │ ├── pysted.base.Objective.get_transmission.rst │ ├── pysted.base.Objective.rst │ ├── pysted.base.RandomActionSelector.rst │ ├── pysted.base.RandomActionSelector.select_action.rst │ ├── pysted.base.TemporalDatamap.bleach_future.rst │ ├── pysted.base.TemporalDatamap.create_t_stack_dmap.rst │ ├── pysted.base.TemporalDatamap.rst │ ├── pysted.base.TemporalDatamap.set_bleached_datamap.rst │ ├── pysted.base.TemporalDatamap.set_roi.rst │ ├── pysted.base.TemporalDatamap.update_dicts.rst │ ├── pysted.base.TemporalDatamap.update_whole_datamap.rst │ ├── pysted.base.TemporalExperiment.play_action.rst │ ├── pysted.base.TemporalExperiment.rst │ ├── pysted.base.TemporalSynapseDmap.bleach_future.rst │ ├── pysted.base.TemporalSynapseDmap.bleach_future_proportional.rst │ ├── pysted.base.TemporalSynapseDmap.create_t_stack_dmap.rst │ ├── pysted.base.TemporalSynapseDmap.create_t_stack_dmap_sampled.rst │ ├── pysted.base.TemporalSynapseDmap.create_t_stack_dmap_smooth.rst │ ├── pysted.base.TemporalSynapseDmap.create_t_stack_dmap_smooth_2.rst │ ├── pysted.base.TemporalSynapseDmap.rst │ ├── pysted.base.TemporalSynapseDmap.set_bleached_datamap.rst │ ├── pysted.base.TemporalSynapseDmap.set_roi.rst │ ├── pysted.base.TemporalSynapseDmap.update_dicts.rst │ ├── pysted.base.TemporalSynapseDmap.update_whole_datamap.rst │ ├── pysted.base.TestTemporalDmap.bleach_future.rst │ ├── pysted.base.TestTemporalDmap.create_t_stack_dmap.rst │ ├── pysted.base.TestTemporalDmap.rst │ ├── pysted.base.TestTemporalDmap.set_bleached_datamap.rst │ ├── pysted.base.TestTemporalDmap.set_roi.rst │ ├── pysted.base.TestTemporalDmap.update_dicts.rst │ ├── pysted.base.TestTemporalDmap.update_whole_datamap.rst │ ├── pysted.base.rst │ ├── pysted.bleach_funcs.default_update_survival_probabilities.rst │ ├── pysted.bleach_funcs.rst │ ├── pysted.bleach_funcs.sample_molecules.rst │ ├── pysted.cUtils.calculate_amplitude.rst │ ├── pysted.cUtils.rst │ ├── pysted.data.loader.DatamapLoader.rst │ ├── pysted.data.loader.rst │ ├── pysted.data.rst │ ├── pysted.exp_data_gen.Beads.generate_frame.rst │ ├── pysted.exp_data_gen.Beads.rst │ ├── pysted.exp_data_gen.Nanodomain.add_flash_curve.rst │ ├── pysted.exp_data_gen.Nanodomain.rst │ ├── pysted.exp_data_gen.Synapse.add_nanodomains.rst │ ├── pysted.exp_data_gen.Synapse.fatten_nanodomains.rst │ ├── pysted.exp_data_gen.Synapse.filter_valid_nanodomain_pos.rst │ ├── pysted.exp_data_gen.Synapse.flash_nanodomains.rst │ ├── pysted.exp_data_gen.Synapse.rotate_and_translate.rst │ ├── pysted.exp_data_gen.Synapse.rst │ ├── pysted.exp_data_gen.degrees_to_radians.rst │ ├── pysted.exp_data_gen.rotate_nds.rst │ ├── pysted.exp_data_gen.rst │ ├── pysted.microscopes.DyMINMicroscope.add_to_pixel_bank.rst │ ├── pysted.microscopes.DyMINMicroscope.cache.rst │ ├── pysted.microscopes.DyMINMicroscope.clear_cache.rst │ ├── pysted.microscopes.DyMINMicroscope.empty_pixel_bank.rst │ ├── pysted.microscopes.DyMINMicroscope.get_effective.rst │ ├── pysted.microscopes.DyMINMicroscope.get_signal_and_bleach.rst │ ├── pysted.microscopes.DyMINMicroscope.is_cached.rst │ ├── pysted.microscopes.DyMINMicroscope.rst │ ├── pysted.microscopes.DyMINMicroscope.take_from_pixel_bank.rst │ ├── pysted.microscopes.DyMINRESCueMicroscope.add_to_pixel_bank.rst │ ├── pysted.microscopes.DyMINRESCueMicroscope.cache.rst │ ├── pysted.microscopes.DyMINRESCueMicroscope.clear_cache.rst │ ├── pysted.microscopes.DyMINRESCueMicroscope.empty_pixel_bank.rst │ ├── pysted.microscopes.DyMINRESCueMicroscope.get_effective.rst │ ├── pysted.microscopes.DyMINRESCueMicroscope.get_signal_and_bleach.rst │ ├── pysted.microscopes.DyMINRESCueMicroscope.is_cached.rst │ ├── pysted.microscopes.DyMINRESCueMicroscope.rst │ ├── pysted.microscopes.DyMINRESCueMicroscope.take_from_pixel_bank.rst │ ├── pysted.microscopes.RESCueMicroscope.add_to_pixel_bank.rst │ ├── pysted.microscopes.RESCueMicroscope.cache.rst │ ├── pysted.microscopes.RESCueMicroscope.clear_cache.rst │ ├── pysted.microscopes.RESCueMicroscope.empty_pixel_bank.rst │ ├── pysted.microscopes.RESCueMicroscope.get_effective.rst │ ├── pysted.microscopes.RESCueMicroscope.get_signal_and_bleach.rst │ ├── pysted.microscopes.RESCueMicroscope.is_cached.rst │ ├── pysted.microscopes.RESCueMicroscope.rst │ ├── pysted.microscopes.RESCueMicroscope.take_from_pixel_bank.rst │ ├── pysted.microscopes.rst │ ├── pysted.raster.raster_func_c_self_bleach_split_g.rst │ ├── pysted.raster.raster_func_dymin.rst │ ├── pysted.raster.raster_func_rescue.rst │ ├── pysted.raster.reset_prob.rst │ ├── pysted.raster.rst │ ├── pysted.rst │ ├── pysted.temporal.Ensemble.append.rst │ ├── pysted.temporal.Ensemble.generate_objects_dict.rst │ ├── pysted.temporal.Ensemble.generate_sequence.rst │ ├── pysted.temporal.Ensemble.reset_force.rst │ ├── pysted.temporal.Ensemble.reset_speed.rst │ ├── pysted.temporal.Ensemble.return_frame.rst │ ├── pysted.temporal.Ensemble.rst │ ├── pysted.temporal.Ensemble.show.rst │ ├── pysted.temporal.Ensemble.spawn.rst │ ├── pysted.temporal.Ensemble.update.rst │ ├── pysted.temporal.Fiber.add_node.rst │ ├── pysted.temporal.Fiber.apply_force.rst │ ├── pysted.temporal.Fiber.apply_jitter.rst │ ├── pysted.temporal.Fiber.generate_random.rst │ ├── pysted.temporal.Fiber.grow.rst │ ├── pysted.temporal.Fiber.reset_force.rst │ ├── pysted.temporal.Fiber.reset_speed.rst │ ├── pysted.temporal.Fiber.return_shape.rst │ ├── pysted.temporal.Fiber.rst │ ├── pysted.temporal.Fiber.spawn.rst │ ├── pysted.temporal.Fiber.update.rst │ ├── pysted.temporal.Nodes.add_node.rst │ ├── pysted.temporal.Nodes.apply_force.rst │ ├── pysted.temporal.Nodes.apply_jitter.rst │ ├── pysted.temporal.Nodes.reset_force.rst │ ├── pysted.temporal.Nodes.reset_speed.rst │ ├── pysted.temporal.Nodes.return_shape.rst │ ├── pysted.temporal.Nodes.rst │ ├── pysted.temporal.Nodes.update.rst │ ├── pysted.temporal.NodesCombiner.add_object.rst │ ├── pysted.temporal.NodesCombiner.apply_force.rst │ ├── pysted.temporal.NodesCombiner.apply_jitter.rst │ ├── pysted.temporal.NodesCombiner.reset_force.rst │ ├── pysted.temporal.NodesCombiner.reset_speed.rst │ ├── pysted.temporal.NodesCombiner.rst │ ├── pysted.temporal.NodesCombiner.update.rst │ ├── pysted.temporal.Polygon.add_node.rst │ ├── pysted.temporal.Polygon.apply_force.rst │ ├── pysted.temporal.Polygon.apply_jitter.rst │ ├── pysted.temporal.Polygon.area.rst │ ├── pysted.temporal.Polygon.expand.rst │ ├── pysted.temporal.Polygon.generate_random.rst │ ├── pysted.temporal.Polygon.reset_force.rst │ ├── pysted.temporal.Polygon.reset_speed.rst │ ├── pysted.temporal.Polygon.return_shape.rst │ ├── pysted.temporal.Polygon.rst │ ├── pysted.temporal.Polygon.update.rst │ ├── pysted.temporal.Synapse.add_object.rst │ ├── pysted.temporal.Synapse.apply_force.rst │ ├── pysted.temporal.Synapse.apply_jitter.rst │ ├── pysted.temporal.Synapse.grow.rst │ ├── pysted.temporal.Synapse.reset_force.rst │ ├── pysted.temporal.Synapse.reset_speed.rst │ ├── pysted.temporal.Synapse.return_shape.rst │ ├── pysted.temporal.Synapse.rst │ ├── pysted.temporal.Synapse.update.rst │ ├── pysted.temporal.rst │ ├── pysted.utils.action_execution.rst │ ├── pysted.utils.action_execution_2.rst │ ├── pysted.utils.action_execution_g.rst │ ├── pysted.utils.add_event.rst │ ├── pysted.utils.approx_binomial.rst │ ├── pysted.utils.array_padder.rst │ ├── pysted.utils.array_unpadder.rst │ ├── pysted.utils.cart2pol.rst │ ├── pysted.utils.complex_quadrature.rst │ ├── pysted.utils.compute_time_correspondances.rst │ ├── pysted.utils.datamap_generator.rst │ ├── pysted.utils.dict_write_func.rst │ ├── pysted.utils.event_reader.rst │ ├── pysted.utils.exponential.rst │ ├── pysted.utils.flash_generator.rst │ ├── pysted.utils.flash_routine.rst │ ├── pysted.utils.float_to_array_verifier.rst │ ├── pysted.utils.fwhm.rst │ ├── pysted.utils.fwhm_donut.rst │ ├── pysted.utils.generate_fiber_with_synapses.rst │ ├── pysted.utils.generate_raster_pixel_list.rst │ ├── pysted.utils.generate_secondary_fibers.rst │ ├── pysted.utils.generate_synapse_flash_dicts.rst │ ├── pysted.utils.generate_synapses_on_fiber.rst │ ├── pysted.utils.generate_synaptic_fibers.rst │ ├── pysted.utils.get_avg_lightcurve.rst │ ├── pysted.utils.get_light_curve.rst │ ├── pysted.utils.hand_crafted_light_curve.rst │ ├── pysted.utils.inverse.rst │ ├── pysted.utils.inverse_exponential.rst │ ├── pysted.utils.make_path_sane.rst │ ├── pysted.utils.molecules_survival.rst │ ├── pysted.utils.molecules_symmetry.rst │ ├── pysted.utils.mse_calculator.rst │ ├── pysted.utils.pad_values.rst │ ├── pysted.utils.pinhole.rst │ ├── pysted.utils.pixel_list_filter.rst │ ├── pysted.utils.pixel_sampling.rst │ ├── pysted.utils.pxsize_comp2.rst │ ├── pysted.utils.pxsize_comp_array_maker.rst │ ├── pysted.utils.pxsize_grid.rst │ ├── pysted.utils.pxsize_ratio.rst │ ├── pysted.utils.rescale.rst │ ├── pysted.utils.rescale_data.rst │ ├── pysted.utils.resize.rst │ ├── pysted.utils.rst │ ├── pysted.utils.sample_light_curve.rst │ ├── pysted.utils.sampled_flash_manipulations.rst │ ├── pysted.utils.savitzky_golay.rst │ ├── pysted.utils.set_starting_pixel.rst │ ├── pysted.utils.shift_data.rst │ ├── pysted.utils.smooth_ramp_hand_crafted_light_curve.rst │ ├── pysted.utils.smooth_ramp_hand_crafted_light_curve_2.rst │ ├── pysted.utils.stack.rst │ ├── pysted.utils.stack_btmod_definitive.rst │ ├── pysted.utils.symmetry_verifier.rst │ └── pysted.utils.time_quantum_to_flash_tstep_correspondance.rst └── requirements.txt ├── examples ├── acquire_noisy.py ├── acquire_singledot.py ├── acquire_stack.py ├── data │ ├── fibres.tif │ └── singledot.tif ├── experiment_example.ini └── kernel.png ├── flash_files ├── events_curves.npy └── stream1_events.txt ├── pySTED_tutorial.py ├── pyproject.toml ├── pysted ├── __init__.py ├── _draw.pyx ├── base.py ├── bleach_funcs.pyx ├── cUtils.c ├── data │ ├── __init__.py │ ├── examples │ │ ├── factin │ │ │ ├── 0.npy │ │ │ ├── 1.npy │ │ │ ├── 2.npy │ │ │ ├── 3.npy │ │ │ ├── 4.npy │ │ │ └── 5.npy │ │ ├── psd95 │ │ │ ├── 0.npy │ │ │ ├── 1.npy │ │ │ ├── 2.npy │ │ │ ├── 4.npy │ │ │ ├── 5.npy │ │ │ └── 6.npy │ │ └── tubulin │ │ │ ├── 0.npy │ │ │ ├── 1.npy │ │ │ ├── 2.npy │ │ │ ├── 3.npy │ │ │ ├── 4.npy │ │ │ └── 5.npy │ └── loader.py ├── exp_data_gen.py ├── microscopes.py ├── raster.pyx ├── temporal.py └── utils.py ├── requirements.txt ├── script_templates ├── general_acq.py └── make_exp_video.py └── 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