.gitignore
.pre-commit-config.yaml
LICENSE
README.md
pyproject.toml
setup.cfg
setup.py
tox.ini
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/documentation.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/plugin_preview.yml
.github/workflows/pytests.yml
.github/workflows/test_and_deploy.yml
docs/__init__.py
docs/recOrder_Installation.md
docs/recOrder_UserGuide.md
docs/images/FlowChart.png
docs/images/HSV_legend.png
docs/images/JCh_Color_legend.png
docs/images/JCh_legend.png
docs/images/acq_diatoms2D.png
docs/images/acq_finished.png
docs/images/acquisition.png
docs/images/advanced.png
docs/images/bg_example.png
docs/images/calib_finished.png
docs/images/cap_bg.png
docs/images/connect_to_mm.png
docs/images/create_group.png
docs/images/create_preset.png
docs/images/flowchart_resize.jpg
docs/images/flowchart_resize.png
docs/images/ideal_plot.png
docs/images/recOrder_Fig1_Overview.png
docs/images/recOrder_logo.jpg
docs/images/recOrder_logo.png
docs/images/recOrder_logo_web.jpg
docs/images/recOrder_logo_web.png
docs/images/recOrder_offline.png
docs/images/recOrder_plugin_logo.png
docs/images/reconstruct_acq.png
docs/images/reconstruct_acq2.png
docs/images/reconstruct_acq_general.png
docs/images/reconstruct_acq_mparams.png
docs/images/reconstruct_acq_reg.png
docs/images/run_calib.png
docs/images/run_port.png
docs/images/switch_online.png
docs/images/tutorial_thumbnail.png
examples/__init__.py
examples/example_configs/config_example_fluor_deconvolution.yml
examples/example_configs/config_example_phase_from_bf.yml
examples/example_configs/config_example_qlipp.yml
examples/notebooks/QLIPP_Calibration_Notebook.ipynb
examples/notebooks/Reconstruction_FluorDeconv.ipynb
examples/notebooks/Reconstruction_PhaseFromBF.ipynb
examples/notebooks/Reconstruction_QLIPP.ipynb
recOrder/__init__.py
recOrder/_version.py
recOrder/napari.yaml
recOrder/acq/__init__.py
recOrder/acq/acq_functions.py
recOrder/calib/Calibration.py
recOrder/calib/Meadowlark_Curves.npy
recOrder/calib/Optimization.py
recOrder/calib/__init__.py
recOrder/calib/mmgr_dal_MeadowlarkLC.csv
recOrder/compute/__init__.py
recOrder/compute/fluorescence_compute.py
recOrder/compute/qlipp_compute.py
recOrder/io/__init__.py
recOrder/io/_reader.py
recOrder/io/config_reader.py
recOrder/io/core_functions.py
recOrder/io/utils.py
recOrder/io/zarr_converter.py
recOrder/pipelines/__init__.py
recOrder/pipelines/base.py
recOrder/pipelines/fluor_deconv_pipeline.py
recOrder/pipelines/phase_from_bf_pipeline.py
recOrder/pipelines/pipeline_manager.py
recOrder/pipelines/qlipp_pipeline.py
recOrder/plugin/__init__.py
recOrder/plugin/qtdesigner/mplwidget.py
recOrder/plugin/qtdesigner/recOrder_ui.py
recOrder/plugin/qtdesigner/recOrder_ui.ui
recOrder/plugin/widget/__init__.py
recOrder/plugin/widget/loading_widget.py
recOrder/plugin/widget/main_widget.py
recOrder/plugin/widget/napari_plugin_entry_point.py
recOrder/plugin/workers/__init__.py
recOrder/plugin/workers/acquisition_workers.py
recOrder/plugin/workers/calibration_workers.py
recOrder/plugin/workers/reconstruction_workers.py
recOrder/postproc/__init__.py
recOrder/postproc/post_processing.py
recOrder/preproc/__init__.py
recOrder/preproc/pre_processing.py
recOrder/scripts/__init__.py
recOrder/scripts/convert_tiff_to_zarr.py
recOrder/scripts/help.py
recOrder/scripts/launch_napari.py
recOrder/scripts/md5_check_sum.py
recOrder/scripts/run_pipeline.py
recOrder/tests/conftest.py
recOrder/tests/config_reader_tests/test_config_reader.py
recOrder/tests/converter_tests/test_converter.py
recOrder/tests/pipeline_tests/test_fluorescence_deconvolution_pipeline.py
recOrder/tests/pipeline_tests/test_phase_from_bf_pipeline.py
recOrder/tests/pipeline_tests/test_pre_post_processing.py
recOrder/tests/pipeline_tests/test_qlipp_pipeline.py
recOrder/tests/pipeline_tests/test_qlipp_pipeline_tiff.py
recOrder/tests/test_configs/config_cli_pytest.yml
recOrder/tests/test_configs/config_postprocessing_pytest.yml
recOrder/tests/test_configs/config_preprocessing_pytest.yml
recOrder/tests/test_configs/fluor_deconv/config_fluor_2D_pytest.yml
recOrder/tests/test_configs/fluor_deconv/config_fluor_3D_pytest.yml
recOrder/tests/test_configs/fluor_deconv/config_fluor_full_pytest.yml
recOrder/tests/test_configs/fluor_deconv/config_fluor_full_registration_pytest.yml
recOrder/tests/test_configs/phase/config_phase_2D_pytest.yml
recOrder/tests/test_configs/phase/config_phase_3D_pytest.yml
recOrder/tests/test_configs/phase/config_phase_full_pytest.yml
recOrder/tests/test_configs/qlipp/config_qlipp_2D_pytest.yml
recOrder/tests/test_configs/qlipp/config_qlipp_2D_pytest_tiff.yml
recOrder/tests/test_configs/qlipp/config_qlipp_full_pytest.yml
recOrder/tests/test_configs/qlipp/config_qlipp_full_pytest_tiff.yml
recOrder/tests/test_configs/qlipp/config_qlipp_full_recon_pytest.yml
recOrder/tests/test_configs/qlipp/config_qlipp_full_recon_pytest_tiff.yml
recOrder_napari.egg-info/PKG-INFO
recOrder_napari.egg-info/SOURCES.txt
recOrder_napari.egg-info/dependency_links.txt
recOrder_napari.egg-info/entry_points.txt
recOrder_napari.egg-info/requires.txt
recOrder_napari.egg-info/top_level.txt