LICENSE
MANIFEST.in
README.md
THIRD_PARTY_NOTICES.md
pyproject.toml
setup.py
ci/smoke.py
csrc/combine.hpp
csrc/cutoff.hpp
csrc/drift.cpp
csrc/drift.hpp
csrc/filters.hpp
csrc/fit.cpp
csrc/global.hpp
csrc/group.cpp
csrc/group.hpp
csrc/linalg.hpp
csrc/lm.hpp
csrc/maxima.hpp
csrc/models.hpp
csrc/neighbours.cpp
csrc/parallel.hpp
csrc/render.cpp
csrc/render.hpp
src/smappy/__init__.py
src/smappy/api.py
src/smappy/astigmatic_z.py
src/smappy/batch.py
src/smappy/beads.py
src/smappy/blocks.py
src/smappy/calibration_list.py
src/smappy/camera.py
src/smappy/camera_db.py
src/smappy/chain.py
src/smappy/columns.py
src/smappy/config.py
src/smappy/correlation.py
src/smappy/detect.py
src/smappy/diagnostics.py
src/smappy/drift.py
src/smappy/dualfit.py
src/smappy/fiducials.py
src/smappy/figures.py
src/smappy/filter.py
src/smappy/fit_rois.py
src/smappy/frametags.py
src/smappy/frc.py
src/smappy/gpu.py
src/smappy/group.py
src/smappy/handoff.py
src/smappy/id_statistics.py
src/smappy/image_processing.py
src/smappy/images.py
src/smappy/layer_registration.py
src/smappy/layer_state.py
src/smappy/live.py
src/smappy/locs.py
src/smappy/lut.py
src/smappy/mathparse.py
src/smappy/mbm.py
src/smappy/mbm_registration.py
src/smappy/metadata.py
src/smappy/microscope_db.py
src/smappy/movie.py
src/smappy/npc.py
src/smappy/params.py
src/smappy/picture.py
src/smappy/pipeline.py
src/smappy/presets.py
src/smappy/psf.py
src/smappy/rawframes.py
src/smappy/rcc.py
src/smappy/region_filter.py
src/smappy/region_maths.py
src/smappy/region_results.py
src/smappy/region_runs.py
src/smappy/region_table.py
src/smappy/regions.py
src/smappy/render.py
src/smappy/scan.py
src/smappy/segmentation.py
src/smappy/session.py
src/smappy/spatial.py
src/smappy/stability.py
src/smappy/torch_install.py
src/smappy/transformation.py
src/smappy/undo.py
src/smappy/updater.py
src/smappy/updates.py
src/smappy/user_plugins.py
src/smappy/view3d.py
src/smappy/view_path.py
src/smappy/workspace.py
src/smappy/_comet/LICENSE.txt
src/smappy/_comet/__init__.py
src/smappy/_comet/_version.py
src/smappy/_comet/core/__init__.py
src/smappy/_comet/core/_dialogs.py
src/smappy/_comet/core/backends.py
src/smappy/_comet/core/cpu_wrapper.py
src/smappy/_comet/core/drift_optimizer.py
src/smappy/_comet/core/interpolation.py
src/smappy/_comet/core/io_utils.py
src/smappy/_comet/core/pair_indices.py
src/smappy/_comet/core/qc_utils.py
src/smappy/_comet/core/segmenter.py
src/smappy/_comet/core/cuda_wrapper/__init__.py
src/smappy/_comet/core/cuda_wrapper/cuda_wrapper.py
src/smappy/_comet/core/cuda_wrapper/cuda_wrapper_qc.py
src/smappy/assistant/__init__.py
src/smappy/assistant/attach.py
src/smappy/assistant/index.py
src/smappy/assistant/knowledge.py
src/smappy/assistant/launch.py
src/smappy/assistant/protocol.py
src/smappy/assistant/server.py
src/smappy/assistant/tools.py
src/smappy/calibrate/__init__.py
src/smappy/calibrate/core.py
src/smappy/calibrate/depth.py
src/smappy/calibrate/dual.py
src/smappy/calibrate/elliptical.py
src/smappy/calibrate/input.py
src/smappy/calibrate/insitu.py
src/smappy/calibrate/insitu_run.py
src/smappy/calibrate/insitu_views.py
src/smappy/calibrate/model_views.py
src/smappy/calibrate/plots.py
src/smappy/calibrate/psf_methods.py
src/smappy/calibrate/psf_window.py
src/smappy/calibrate/pupil.py
src/smappy/calibrate/qt_gui.py
src/smappy/calibrate/stack_browser.py
src/smappy/calibrate/stack_view.py
src/smappy/calibrate/transform.py
src/smappy/calibrate/validation.py
src/smappy/cli/__init__.py
src/smappy/cli/batch.py
src/smappy/cli/calibrate.py
src/smappy/cli/camera_args.py
src/smappy/cli/drift.py
src/smappy/cli/fit.py
src/smappy/cli/gui.py
src/smappy/data/default.gui.yaml
src/smappy/data/microscopes.json
src/smappy/data/csv_conversions/SMAP.yaml
src/smappy/data/csv_conversions/ThunderSTORM.yaml
src/smappy/data/icons/smappy.svg
src/smappy/data/icons/smappy_128.png
src/smappy/data/icons/smappy_16.png
src/smappy/data/icons/smappy_24.png
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src/smappy/data/icons/smappy_48.png
src/smappy/data/icons/smappy_512.png
src/smappy/data/icons/smappy_64.png
src/smappy/data/segment_presets/CME.yaml
src/smappy/data/segment_presets/Circles.yaml
src/smappy/data/segment_presets/NPC.yaml
src/smappy/data/simulation_components/NPC (Nup96).yaml
src/smappy/data/simulation_components/background.yaml
src/smappy/data/simulation_components/beads.yaml
src/smappy/data/simulation_components/diffusing particles.yaml
src/smappy/data/simulation_presets/Diffusion.yaml
src/smappy/data/simulation_presets/Filaments.yaml
src/smappy/data/simulation_presets/Nuclear pores (Nup96).yaml
src/smappy/data/simulation_presets/Pores with beads.yaml
src/smappy/data/simulation_presets/Ring and cross (two colours).yaml
src/smappy/data/simulation_presets/Two-colour pores.yaml
src/smappy/data/simulation_presets/Two-state diffusion.yaml
src/smappy/data/structures/cross.yaml
src/smappy/data/structures/demo.yaml
src/smappy/data/structures/filaments.yaml
src/smappy/data/structures/npc.yaml
src/smappy/data/structures/pie.yaml
src/smappy/data/structures/ring.yaml
src/smappy/data/user_plugins/AGENTS.md.in
src/smappy/data/user_plugins/CLAUDE.md.in
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src/smappy/data/user_plugins/template.py.in
src/smappy/docs/__init__.py
src/smappy/docs/__main__.py
src/smappy/docs/markup.py
src/smappy/docs/panels/3D view.md
src/smappy/docs/panels/Assistant.md
src/smappy/docs/panels/Batch window.md
src/smappy/docs/panels/Bead calibration.md
src/smappy/docs/panels/Bead selector.md
src/smappy/docs/panels/Camera editor.md
src/smappy/docs/panels/Glossary.md
src/smappy/docs/panels/Microscope manager.md
src/smappy/docs/panels/PSF calibration.md
src/smappy/docs/panels/ROI manager.md
src/smappy/docs/panels/Regions tab.md
src/smappy/docs/panels/Render tab.md
src/smappy/docs/panels/Your own plugins.md
src/smappy/gui/__init__.py
src/smappy/gui/about.py
src/smappy/gui/app.py
src/smappy/gui/assistant_pane.py
src/smappy/gui/assistant_server.py
src/smappy/gui/batch_window.py
src/smappy/gui/bead_window.py
src/smappy/gui/camera_editor.py
src/smappy/gui/camera_view.py
src/smappy/gui/canvas.py
src/smappy/gui/chain_panel.py
src/smappy/gui/chooser.py
src/smappy/gui/collector.py
src/smappy/gui/dialogs.py
src/smappy/gui/drops.py
src/smappy/gui/errors.py
src/smappy/gui/figures.py
src/smappy/gui/folders.py
src/smappy/gui/help_window.py
src/smappy/gui/icon.py
src/smappy/gui/identity.py
src/smappy/gui/live_session.py
src/smappy/gui/mac_panel.py
src/smappy/gui/merging.py
src/smappy/gui/microscope_editor.py
src/smappy/gui/microscope_form.py
src/smappy/gui/microscope_view.py
src/smappy/gui/msr_import.py
src/smappy/gui/params.py
src/smappy/gui/plugin_panel.py
src/smappy/gui/plugin_tab.py
src/smappy/gui/preferences.py
src/smappy/gui/region_filter_panel.py
src/smappy/gui/region_steps.py
src/smappy/gui/render_tab.py
src/smappy/gui/render_view.py
src/smappy/gui/roi_annotate.py
src/smappy/gui/roi_ranges.py
src/smappy/gui/roi_site.py
src/smappy/gui/roi_tab.py
src/smappy/gui/roi_window.py
src/smappy/gui/scan_player.py
src/smappy/gui/screen.py
src/smappy/gui/shape_tools.py
src/smappy/gui/updates.py
src/smappy/gui/view3d.py
src/smappy/gui/widgets.py
src/smappy/io/__init__.py
src/smappy/io/blosc.py
src/smappy/io/calibration.py
src/smappy/io/conversions.py
src/smappy/io/decode.py
src/smappy/io/emu.py
src/smappy/io/formats.py
src/smappy/io/hdf5.py
src/smappy/io/mcos.py
src/smappy/io/minflux.py
src/smappy/io/msr.py
src/smappy/io/ndtiff.py
src/smappy/io/obf.py
src/smappy/io/picasso.py
src/smappy/io/queue_source.py
src/smappy/io/singles.py
src/smappy/io/tiff.py
src/smappy/io/watch.py
src/smappy/io/zarr_lite.py
src/smappy/plugins/__init__.py
src/smappy/plugins/after_fit.py
src/smappy/plugins/assign_colors.py
src/smappy/plugins/astigmatic_z.py
src/smappy/plugins/average_rois.py
src/smappy/plugins/bead_calibration.py
src/smappy/plugins/blinking.py
src/smappy/plugins/chain_layers.py
src/smappy/plugins/circle_fit.py
src/smappy/plugins/cluster_shape.py
src/smappy/plugins/clusters.py
src/smappy/plugins/combine_files.py
src/smappy/plugins/curves.py
src/smappy/plugins/discovery.py
src/smappy/plugins/drift_comet.py
src/smappy/plugins/drift_fiducials.py
src/smappy/plugins/drift_mbm.py
src/smappy/plugins/drift_rcc.py
src/smappy/plugins/drift_result.py
src/smappy/plugins/file.py
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src/smappy/plugins/ground_truth.py
src/smappy/plugins/histogram.py
src/smappy/plugins/history.py
src/smappy/plugins/id_statistics.py
src/smappy/plugins/image_tags.py
src/smappy/plugins/line_profile.py
src/smappy/plugins/link_tracks.py
src/smappy/plugins/math_parser.py
src/smappy/plugins/mbm_registration.py
src/smappy/plugins/neighbourhood.py
src/smappy/plugins/npc.py
src/smappy/plugins/npc_analysis.chain.yaml
src/smappy/plugins/precision.py
src/smappy/plugins/process_image.py
src/smappy/plugins/psf_calibration.py
src/smappy/plugins/region_column.py
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src/smappy/plugins/region_filter.py
src/smappy/plugins/register_layers.py
src/smappy/plugins/registration.py
src/smappy/plugins/remove_locs.py
src/smappy/plugins/roi.py
src/smappy/plugins/roi_centre.py
src/smappy/plugins/roi_images.py
src/smappy/plugins/roi_order.py
src/smappy/plugins/segment.py
src/smappy/plugins/shuffle_ids.py
src/smappy/plugins/simulate.py
src/smappy/plugins/spatial_statistics.py
src/smappy/plugins/stability.py
src/smappy/plugins/statistics.py
src/smappy/plugins/time_course.py
src/smappy/plugins/tracking_analysis.py
src/smappy/plugins/transform.py
src/smappy/plugins/docs/Analysis/After fit/After the fit.md
src/smappy/plugins/docs/Analysis/After fit/Assign colours.md
src/smappy/plugins/docs/Analysis/After fit/Astigmatic z.md
src/smappy/plugins/docs/Analysis/Drift/COMET.md
src/smappy/plugins/docs/Analysis/Drift/Fiducials.md
src/smappy/plugins/docs/Analysis/Drift/MBM.md
src/smappy/plugins/docs/Analysis/Drift/RCC.md
src/smappy/plugins/docs/Analysis/Measure/Blinking.md
src/smappy/plugins/docs/Analysis/Measure/Circle fit.md
src/smappy/plugins/docs/Analysis/Measure/Cluster shape.md
src/smappy/plugins/docs/Analysis/Measure/Ground Truth.md
src/smappy/plugins/docs/Analysis/Measure/Histogram.md
src/smappy/plugins/docs/Analysis/Measure/Id statistics.md
src/smappy/plugins/docs/Analysis/Measure/Line Profile.md
src/smappy/plugins/docs/Analysis/Measure/Localization Precision.md
src/smappy/plugins/docs/Analysis/Measure/Localization Statistics.md
src/smappy/plugins/docs/Analysis/Measure/NPC Corners.md
src/smappy/plugins/docs/Analysis/Measure/Spatial statistics.md
src/smappy/plugins/docs/Analysis/Measure/Stability.md
src/smappy/plugins/docs/Analysis/Measure/Time Course.md
src/smappy/plugins/docs/Analysis/Process/Combine files.md
src/smappy/plugins/docs/Analysis/Process/History.md
src/smappy/plugins/docs/Analysis/Process/Image Tags.md
src/smappy/plugins/docs/Analysis/Process/Layers.md
src/smappy/plugins/docs/Analysis/Process/Math Parser.md
src/smappy/plugins/docs/Analysis/Process/Neighbourhood.md
src/smappy/plugins/docs/Analysis/Process/Process image.md
src/smappy/plugins/docs/Analysis/Process/Remove Localizations.md
src/smappy/plugins/docs/Analysis/Process/Shuffle ids.md
src/smappy/plugins/docs/Analysis/Process/Transform.md
src/smappy/plugins/docs/Analysis/Regions/Average ROIs.md
src/smappy/plugins/docs/Analysis/Regions/Centre ROIs.md
src/smappy/plugins/docs/Analysis/Regions/Filter ROIs.md
src/smappy/plugins/docs/Analysis/Regions/Filter regions.md
src/smappy/plugins/docs/Analysis/Regions/Find clusters.md
src/smappy/plugins/docs/Analysis/Regions/Regions to column.md
src/smappy/plugins/docs/Analysis/Regions/Remove double ROIs.md
src/smappy/plugins/docs/Analysis/Regions/Segment regions.md
src/smappy/plugins/docs/Analysis/Regions/Sort ROIs.md
src/smappy/plugins/docs/Analysis/Regions/Summarize/Curves.md
src/smappy/plugins/docs/Analysis/Regions/Summarize/Export table.md
src/smappy/plugins/docs/Analysis/Regions/Summarize/Histograms.md
src/smappy/plugins/docs/Analysis/Regions/Summarize/NPC labelling efficiency.md
src/smappy/plugins/docs/Analysis/Regions/Workflow/NPC Analysis.md
src/smappy/plugins/docs/Analysis/Register/Calibrate transform.md
src/smappy/plugins/docs/Analysis/Register/MBM registration.md
src/smappy/plugins/docs/Analysis/Register/Register layers.md
src/smappy/plugins/docs/Analysis/Tracking/Link tracks.md
src/smappy/plugins/docs/Analysis/Tracking/Tracking analysis.md
src/smappy/plugins/docs/File/Export/Image.md
src/smappy/plugins/docs/File/Export/Localizations.md
src/smappy/plugins/docs/File/Export/ROI images.md
src/smappy/plugins/docs/File/Export/Stack.md
src/smappy/plugins/docs/File/Load/Auto.md
src/smappy/plugins/docs/File/Load/Load.md
src/smappy/plugins/docs/File/Save/smappy HDF5.md
src/smappy/plugins/docs/File/Simulate/Simulate.md
src/smappy/plugins/docs/Localize/Bead calibration.md
src/smappy/plugins/docs/Localize/Gaussian 2D 2C.md
src/smappy/plugins/docs/Localize/Gaussian 2D.md
src/smappy/plugins/docs/Localize/PSF calibration.md
src/smappy/plugins/docs/Localize/Spline 3D 2C.md
src/smappy/plugins/docs/Localize/Spline 3D.md
src/smappy/roi_manager/__init__.py
src/smappy/roi_manager/core.py
src/smappy/roi_manager/order.py
src/smappy/roi_manager/pipeline.py
src/smappy/simulate/__init__.py
src/smappy/simulate/beads.py
src/smappy/simulate/camera.py
src/smappy/simulate/kinetics.py
src/smappy/simulate/localizations.py
src/smappy/simulate/scene.py
src/smappy/simulate/settings.py
src/smappy/simulate/source.py
src/smappy/simulate/structure.py
src/smappy/simulate/tracks.py
src/smappy/tracking/__init__.py
src/smappy/tracking/analysis.py
src/smappy/tracking/columns.py
src/smappy/tracking/link.py
src/smappy/tutorial/__init__.py
src/smappy/tutorial/__main__.py
src/smappy/tutorial/director.py
src/smappy/tutorial/player.py
src/smappy/tutorial/voice.py
src/smappy/tutorial/topics/__init__.py
src/smappy/tutorial/topics/assistant.py
src/smappy/tutorial/topics/batch.py
src/smappy/tutorial/topics/common.py
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src/smappy/tutorial/topics/fitting_3d.py
src/smappy/tutorial/topics/layout.py
src/smappy/tutorial/topics/measuring.py
src/smappy/tutorial/topics/own_plugins.py
src/smappy/tutorial/topics/plugins.py
src/smappy/tutorial/topics/quickstart.py
src/smappy/tutorial/topics/rendering.py
src/smappy/tutorial/topics/simulation.py
src/smappy/tutorial/topics/two_colour.py
src/smappy/tutorial/topics/two_colour_3d.py
src/smappy_smlm.egg-info/PKG-INFO
src/smappy_smlm.egg-info/SOURCES.txt
src/smappy_smlm.egg-info/dependency_links.txt
src/smappy_smlm.egg-info/entry_points.txt
src/smappy_smlm.egg-info/requires.txt
src/smappy_smlm.egg-info/top_level.txt
src/uipsf/LICENSE
src/uipsf/__init__.py
src/uipsf/device.py
src/uipsf/movie.py
src/uipsf/noise.py
src/uipsf/params.py
src/uipsf/simulate.py
src/uipsf/data/__init__.py
src/uipsf/data/dataset.py
src/uipsf/diagnostics/__init__.py
src/uipsf/diagnostics/atlas.py
src/uipsf/diagnostics/camera.py
src/uipsf/diagnostics/figures.py
src/uipsf/diagnostics/halves.py
src/uipsf/diagnostics/heldout.py
src/uipsf/diagnostics/probes.py
src/uipsf/export/__init__.py
src/uipsf/export/model_file.py
src/uipsf/model/__init__.py
src/uipsf/model/astig.py
src/uipsf/model/background.py
src/uipsf/model/channels.py
src/uipsf/model/forward.py
src/uipsf/model/geometry.py
src/uipsf/model/intensity.py
src/uipsf/model/psf.py
src/uipsf/model/pupil.py
src/uipsf/model/start.py
src/uipsf/optics/__init__.py
src/uipsf/optics/grid.py
src/uipsf/optics/kernels.py
src/uipsf/optics/layers.py
src/uipsf/optics/mdft.py
src/uipsf/optics/system.py
src/uipsf/optics/vectorial.py
src/uipsf/optics/zernike.py
src/uipsf/solve/__init__.py
src/uipsf/solve/blocks.py
src/uipsf/solve/cg.py
src/uipsf/solve/lbfgs.py
src/uipsf/solve/lm.py
src/uipsf/solve/problem.py
src/uipsf/solve/result.py
src/uipsf/workflows/__init__.py
src/uipsf/workflows/beads.py
src/uipsf/workflows/calibrate.py
src/uipsf/workflows/insitu.py
src/uipsf/workflows/insitu_rounds.py
src/uipsf/workflows/rejection.py
src/uipsf/workflows/scoring.py
src/uipsf/workflows/spline.py
tests/conftest.py
tests/test_api.py
tests/test_append.py
tests/test_assign_colors.py
tests/test_assistant.py
tests/test_assistant_gui.py
tests/test_astigmatic_z.py
tests/test_average_rois.py
tests/test_batch.py
tests/test_batch_foundations.py
tests/test_bead_calibration.py
tests/test_beads.py
tests/test_blinking.py
tests/test_blocks.py
tests/test_calibrate_qt.py
tests/test_calibration.py
tests/test_calibration_list.py
tests/test_camera_db.py
tests/test_camera_editor.py
tests/test_camera_frames.py
tests/test_camera_view.py
tests/test_chain.py
tests/test_chain_gui.py
tests/test_changes_locs.py
tests/test_channel_transform.py
tests/test_chooser.py
tests/test_circle_fit.py
tests/test_cluster_shape.py
tests/test_clusters.py
tests/test_collector.py
tests/test_context.py
tests/test_control_width.py
tests/test_copy.py
tests/test_curves.py
tests/test_detach.py
tests/test_detect_roi.py
tests/test_diagnostics.py
tests/test_discovery.py
tests/test_drift.py
tests/test_drift_transformation.py
tests/test_drop_files.py
tests/test_dual_calibration.py
tests/test_dual_fit.py
tests/test_dual_gauss_fit.py
tests/test_emu.py
tests/test_err_columns.py
tests/test_errors.py
tests/test_export_image.py
tests/test_extensions.py
tests/test_fiducials.py
tests/test_figure_window.py
tests/test_file_metadata.py
tests/test_file_plugins.py
tests/test_filter.py
tests/test_fit_finish.py
tests/test_fit_plugin.py
tests/test_fit_region.py
tests/test_fitter.py
tests/test_foreign_formats.py
tests/test_formats.py
tests/test_frame_time.py
tests/test_frametags.py
tests/test_frc.py
tests/test_global_fit.py
tests/test_global_gauss.py
tests/test_gpu.py
tests/test_ground_truth.py
tests/test_group.py
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