.git-blame-ignore-revs
.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
CITATION.cff
CONTRIBUTING.md
LICENSE
README.md
pyproject.toml
readme.png
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/documentation.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/pr.yml
.github/workflows/test.yml
docs/README.md
docs/__init__.py
docs/api.rst
docs/conf.py
docs/contact_us.rst
docs/examples.rst
docs/guide.rst
docs/index.rst
docs/_static/switcher.json
docs/_static/waveorder.ico
docs/_static/waveorder.png
docs/_static/css/custom.css
docs/_static/images/JCh_Color_legend.png
docs/_static/images/advanced.png
docs/_static/images/cap_bg.png
docs/_static/images/cli_structure.png
docs/_static/images/comms_video_screenshot.png
docs/_static/images/connect_to_mm.png
docs/_static/images/create_group.png
docs/_static/images/create_group_voltage.png
docs/_static/images/create_preset.png
docs/_static/images/create_preset_voltage.png
docs/_static/images/ideal_plot.png
docs/_static/images/modulation.png
docs/_static/images/no-overlay.png
docs/_static/images/overlay-demo.png
docs/_static/images/overlay.png
docs/_static/images/poincare_swing.svg
docs/_static/images/reconstruction_birefriengence.png
docs/_static/images/reconstruction_data.png
docs/_static/images/reconstruction_data_info.png
docs/_static/images/reconstruction_models.png
docs/_static/images/reconstruction_queue.png
docs/_static/images/run_calib.png
docs/_static/images/run_port.png
docs/_static/images/waveorder_Fig1_Overview.png
docs/api/settings.rst
docs/api/stokes.rst
docs/examples/README.md
docs/examples/configs/README.md
docs/examples/configs/birefringence-and-phase.yml
docs/examples/configs/birefringence.yml
docs/examples/configs/fluorescence.yml
docs/examples/configs/phase.yml
docs/examples/demos/README.md
docs/examples/demos/QLIPP/QLIPP_simulation.ipynb
docs/examples/demos/QLIPP/QLIPP_simulation.py
docs/examples/demos/QPI_defocus/QPI_defocus_experiment.ipynb
docs/examples/demos/QPI_defocus/QPI_defocus_experiment.py
docs/examples/demos/QPI_defocus/QPI_defocus_simulation.ipynb
docs/examples/demos/QPI_defocus/QPI_defocus_simulation.py
docs/examples/deprecated/PTI_experiment/PTI_Experiment_Recon3D_anisotropic_target_small.py
docs/examples/deprecated/PTI_experiment/PTI_full_FOV_anisotropic_target.ipynb
docs/examples/deprecated/PTI_experiment/PTI_full_FOV_cardiac_muscle.ipynb
docs/examples/deprecated/PTI_experiment/PTI_full_FOV_cardiomyocyte_infected_1.ipynb
docs/examples/deprecated/PTI_experiment/PTI_full_FOV_cardiomyocyte_infected_2.ipynb
docs/examples/deprecated/PTI_experiment/PTI_full_FOV_cardiomyocyte_mock.ipynb
docs/examples/deprecated/PTI_experiment/PTI_full_FOV_human_uterus.ipynb
docs/examples/deprecated/PTI_experiment/PTI_full_FOV_mouse_brain_aco.ipynb
docs/examples/deprecated/PTI_experiment/README.md
docs/examples/deprecated/QLIPP_experiment/2D_QLIPP_recon_experiment.ipynb
docs/examples/deprecated/QLIPP_experiment/3D_QLIPP_recon_experiment.ipynb
docs/examples/deprecated/fluorescence_deconvolution/fluorescence_deconv.ipynb
docs/examples/maintenance/README.md
docs/examples/maintenance/PTI_simulation/PTI_Simulation_Forward_2D3D.py
docs/examples/maintenance/PTI_simulation/PTI_Simulation_Recon2D.py
docs/examples/maintenance/PTI_simulation/PTI_Simulation_Recon3D.py
docs/examples/maintenance/PTI_simulation/PTI_formulation.html
docs/examples/maintenance/PTI_simulation/README.md
docs/examples/maintenance/QLIPP_simulation/2D_QLIPP_forward.py
docs/examples/maintenance/QLIPP_simulation/2D_QLIPP_recon.py
docs/examples/models/README.md
docs/examples/models/inplane_oriented_thick_pol3d.py
docs/examples/models/inplane_oriented_thick_pol3d_vector.py
docs/examples/models/isotropic_fluorescent_thick_3d.py
docs/examples/models/isotropic_fluorescent_thin_3d.py
docs/examples/models/isotropic_thin_3d.py
docs/examples/models/phase_thick_3d.py
docs/examples/visuals/README.rst
docs/examples/visuals/plot_greens_tensor.py
docs/examples/visuals/plot_vector_transfer_function_support.py
docs/guide/QLIPP.md
docs/guide/buyers-guide.md
docs/guide/calibration-guide.md
docs/guide/data-schema.md
docs/guide/development-guide.md
docs/guide/microscope-installation-guide.md
docs/guide/napari-plugin-guide.md
docs/guide/reconstruction-guide.md
docs/guide/software-installation-guide.md
docs/scripts/fix_md_links.py
docs/valuable-prs/2023-02-27.110.pr.open.md
tests/__init__.py
tests/conftest.py
tests/test_correction.py
tests/test_examples.py
tests/test_filter.py
tests/test_focus_estimator.py
tests/test_optics.py
tests/test_sampling.py
tests/test_stokes.py
tests/test_util.py
tests/calibration_tests/test_calibration.py
tests/cli_tests/test_cli.py
tests/cli_tests/test_compute_tf.py
tests/cli_tests/test_parsing.py
tests/cli_tests/test_reconstruct.py
tests/cli_tests/test_settings.py
tests/cli_tests/test_zarr_v3_reconstruct.py
tests/mmcore_tests/test_core_func.py
tests/models/test_inplane_oriented_thick_pol3D.py
tests/models/test_isotropic_fluorescent_thick_3d.py
tests/models/test_isotropic_fluorescent_thin_3d.py
tests/models/test_isotropic_thin_3d.py
tests/models/test_phase_thick_3d.py
tests/util_tests/test_create_empty.py
tests/util_tests/test_io.py
tests/util_tests/test_overlays.py
tests/widget_tests/test_dock_widget.py
tests/widget_tests/test_reconstruction_tab_click.py
tests/widget_tests/test_sample_contributions.py
waveorder/__init__.py
waveorder/_version.py
waveorder/background_estimator.py
waveorder/correction.py
waveorder/filter.py
waveorder/focus.py
waveorder/napari.yaml
waveorder/optics.py
waveorder/reconstruct.py
waveorder/sampling.py
waveorder/stokes.py
waveorder/util.py
waveorder/waveorder_reconstructor.py
waveorder/waveorder_simulator.py
waveorder.egg-info/PKG-INFO
waveorder.egg-info/SOURCES.txt
waveorder.egg-info/dependency_links.txt
waveorder.egg-info/entry_points.txt
waveorder.egg-info/requires.txt
waveorder.egg-info/top_level.txt
waveorder/acq/__init__.py
waveorder/acq/acq_functions.py
waveorder/assets/HSV_legend.png
waveorder/assets/JCh_legend.png
waveorder/assets/waveorder_plugin_logo.png
waveorder/calib/Calibration.py
waveorder/calib/Optimization.py
waveorder/calib/__init__.py
waveorder/calib/calibration_workers.py
waveorder/cli/apply_inverse_models.py
waveorder/cli/apply_inverse_transfer_function.py
waveorder/cli/compute_transfer_function.py
waveorder/cli/gui_widget.py
waveorder/cli/main.py
waveorder/cli/monitor.py
waveorder/cli/option_eat_all.py
waveorder/cli/parsing.py
waveorder/cli/printing.py
waveorder/cli/reconstruct.py
waveorder/cli/settings.py
waveorder/cli/utils.py
waveorder/io/__init__.py
waveorder/io/_reader.py
waveorder/io/core_functions.py
waveorder/io/metadata_reader.py
waveorder/io/utils.py
waveorder/io/visualization.py
waveorder/models/inplane_oriented_thick_pol3d.py
waveorder/models/inplane_oriented_thick_pol3d_vector.py
waveorder/models/isotropic_fluorescent_thick_3d.py
waveorder/models/isotropic_fluorescent_thin_3d.py
waveorder/models/isotropic_thin_3d.py
waveorder/models/phase_thick_3d.py
waveorder/plugin/__init__.py
waveorder/plugin/gui.py
waveorder/plugin/gui.ui
waveorder/plugin/job_manager.py
waveorder/plugin/main_widget.py
waveorder/plugin/tab_recon.py
waveorder/scripts/__init__.py
waveorder/scripts/launch_napari.py
waveorder/scripts/repeat-cal-acq-rec.py
waveorder/scripts/repeat-calibration.py
waveorder/scripts/samples.py
waveorder/scripts/simulate_zarr_acq.py
waveorder/visuals/jupyter_visuals.py
waveorder/visuals/matplotlib_visuals.py
waveorder/visuals/napari_visuals.py
waveorder/visuals/utils.py