├── .coveragerc ├── .github └── workflows │ └── piscat.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Fig │ ├── DRA.png │ ├── PiSCAT_NM.png │ ├── PiSCAT_logo.png │ ├── PiSCAT_logo_bg.png │ ├── PiSCAT_structure.png │ ├── cpFPN.png │ ├── fFPN.png │ ├── flowchart.png │ ├── mFPN.png │ ├── tu1_vid1.png │ ├── tu1_vid2.png │ ├── tu2_vid1.png │ ├── tu3_vid1.png │ ├── tu3_vid2.png │ ├── tu4_vid1.png │ ├── tu4_vid2.png │ ├── tu4_vid3_1.png │ ├── tu4_vid4.png │ └── tu4_vid5.png ├── Makefile ├── README.md ├── Tutorial1 │ ├── Tutorial1.md │ └── output_10_1.png ├── Tutorial2 │ ├── Tutorial2.md │ └── output_7_0.png ├── Tutorial3 │ ├── Tutorial3.md │ ├── output_21_1.png │ └── output_7_0.png ├── Tutorial4 │ ├── Tutorial4.md │ ├── output_20_1.png │ ├── output_30_0.png │ └── output_32_0.png ├── Tutorial_UAI_1 │ ├── Tutorial_UAI_1.md │ ├── img_1.png │ ├── img_2.png │ ├── img_3.png │ ├── img_4.png │ └── img_5.png ├── Tutorial_UAI_2 │ ├── Tutorial_UAI_2.md │ ├── img_1.png │ ├── img_2.png │ ├── img_3.png │ ├── img_4.png │ ├── img_5.png │ └── output_13_0.png ├── _static │ └── widestyle.css ├── appendix.rst ├── bibliography.rst ├── cite_us.rst ├── code_reference.rst ├── conf.py ├── download_tutorial_data.md ├── index.rst ├── installation.rst ├── make.bat ├── plugin_UAI.rst ├── references.bib ├── requirements.txt └── tutorials.rst ├── piscat ├── Analysis │ ├── __init__.py │ ├── analysis_protein_histogram.py │ ├── analysis_protein_videos.py │ └── plot_protein_histogram.py ├── BackgroundCorrection │ ├── DRA.py │ ├── __init__.py │ └── noise_floor.py ├── GUI │ ├── BackgroundCorrection │ │ ├── DRA.py │ │ ├── __init__.py │ │ └── fun_bgCorrection.py │ ├── BatchAnalysis │ │ ├── __init__.py │ │ ├── batch_data.py │ │ ├── tab_analysis_protein.py │ │ ├── tab_bg_correction.py │ │ ├── tab_localization.py │ │ ├── tab_plot_histogram.py │ │ ├── tab_reading_data.py │ │ └── tab_trajectory.py │ ├── CPU_Configurations │ │ ├── Import_configuration.py │ │ ├── __init__.py │ │ └── fun_CPU.py │ ├── InputOutput │ │ ├── __init__.py │ │ ├── fun_reading.py │ │ ├── help.py │ │ ├── import_RAW.py │ │ ├── import_im2vid.py │ │ ├── save_GUI.py │ │ └── video_cropping.py │ ├── Memory │ │ ├── __init__.py │ │ └── video_in_memory.py │ ├── Proccessing │ │ ├── __init__.py │ │ └── spectrum.py │ ├── ProgressBar │ │ ├── __init__.py │ │ └── fun_progressBar.py │ ├── Projects │ │ ├── Protein │ │ │ ├── GUI_Protein.py │ │ │ ├── Noise_floor.py │ │ │ └── __init__.py │ │ ├── __init__.py │ │ ├── iPSF │ │ │ ├── __init__.py │ │ │ └── iPSF_model.py │ │ ├── tab_bg_correction.py │ │ ├── tab_localization.py │ │ ├── tab_plot_histogram.py │ │ └── tab_trajectory.py │ ├── VideoAnalysis │ │ ├── __init__.py │ │ ├── video_analysis.py │ │ └── video_calculator.py │ ├── Visualization │ │ ├── __init__.py │ │ ├── contrast_adjustment_GUI.py │ │ ├── fun_display_localization.py │ │ ├── image_viewer.py │ │ ├── play_setting.py │ │ ├── slice_view.py │ │ ├── temporal_annotation_setting.py │ │ └── updating_plots.py │ ├── __init__.py │ ├── annotation │ │ ├── __init__.py │ │ ├── annotation.py │ │ └── line_annotate.py │ ├── icons │ │ ├── Nano.ico │ │ ├── PiSCAT_logo_bg.png │ │ ├── Thumbs.db │ │ ├── __init__.py │ │ ├── movie.gif │ │ └── mpl.png │ └── main.py ├── InputOutput │ ├── __init__.py │ ├── camera_setting.py │ ├── cpu_configurations.py │ ├── gpu_configurations.py │ ├── image_to_video.py │ ├── read_status_line.py │ ├── read_write_data.py │ ├── reading_videos.py │ └── write_video.py ├── Localization │ ├── __init__.py │ ├── data_handling.py │ ├── directional_intensity.py │ ├── gaussian_2D_fit.py │ ├── localization_filtering.py │ ├── particle_localization.py │ └── radial_symmetry_centering.py ├── Plugins │ ├── __init__.py │ └── __main__.py ├── Preproccessing │ ├── FPNc.py │ ├── __init__.py │ ├── applying_mask.py │ ├── filtering.py │ ├── normalization.py │ └── patch_genrator.py ├── Trajectory │ ├── __init__.py │ ├── data_handling.py │ ├── particle_linking.py │ └── temporal_filtering.py ├── Tutorials │ ├── JupyterFiles │ │ ├── Fig │ │ │ ├── DRA.png │ │ │ ├── cpFPN.png │ │ │ ├── fFPN.PNG │ │ │ ├── flowchart.PNG │ │ │ ├── mFPN.png │ │ │ ├── tu2_noise_floor.png │ │ │ └── tu3_noise_floor.png │ │ ├── README.md │ │ ├── Tutorial1.ipynb │ │ ├── Tutorial2.ipynb │ │ ├── Tutorial3.ipynb │ │ ├── Tutorial4.ipynb │ │ ├── Tutorial5.ipynb │ │ ├── Tutorial_CPU_GPU_configurartion.ipynb │ │ ├── Tutorial_UAI_1.ipynb │ │ └── Tutorial_UAI_2.ipynb │ ├── __init__.py │ ├── __main__.py │ └── startup.py ├── Visualization │ ├── __init__.py │ ├── contrast_adjustment.py │ ├── display.py │ ├── display_html.py │ ├── display_jupyter.py │ ├── plot.py │ └── print_colors.py ├── __init__.py ├── __main__.py ├── iPSF_model │ ├── ImagingSetupParameters.py │ ├── L_theta.py │ ├── ScatteredFieldDifferentialPhase.py │ ├── VectorialDiffractionIntegral.py │ └── __init__.py └── utils.py ├── pyproject.toml ├── requirements.txt ├── setup.cfg ├── setup.py └── tests ├── Module ├── .coveragerc ├── Analysis │ ├── analysis_protein_histogram_test.py │ └── analysis_protein_videos_test.py ├── BackgroundCorrection │ ├── DRA_test.py │ └── noise_floor_test.py ├── InputOutput │ ├── camera_setting_test.py │ ├── cpu_configurations_test.py │ ├── gpu_configurations_test.py │ ├── image_to_video_test.py │ ├── read_status_line_test.py │ ├── read_write_data_test.py │ ├── reading_videos_test.py │ └── write_video_test.py ├── Localization │ ├── directional_intensity_test.py │ ├── localization_filtering_test.py │ └── particle_localization_test.py ├── Preproccessing │ ├── FPNc_test.py │ ├── applying_mask_test.py │ ├── filtering_test.py │ ├── normalization_test.py │ └── patch_genrator_test.py └── Trajectory │ ├── data_handling_test.py │ ├── particle_linking_test.py │ └── temporal_filtering_test.py ├── README.md ├── __init__.py └── test_smoke.py /.coveragerc: -------------------------------------------------------------------------------- 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