├── .github ├── dependabot.yml ├── lint │ └── action.yml └── workflows │ └── test_and_deploy.yml ├── .gitignore ├── .zenodo.json ├── LICENSE ├── MANIFEST.in ├── README.md ├── core ├── lls_core │ ├── __init__.py │ ├── cmds │ │ ├── __init__.py │ │ └── __main__.py │ ├── config.py │ ├── cropping.py │ ├── deconvolution.py │ ├── llsz_core.py │ ├── models │ │ ├── __init__.py │ │ ├── crop.py │ │ ├── deconvolution.py │ │ ├── deskew.py │ │ ├── lattice_data.py │ │ ├── output.py │ │ ├── results.py │ │ └── utils.py │ ├── sample │ │ ├── LLS7_t1_ch1.czi │ │ ├── LLS7_t1_ch3.czi │ │ ├── LLS7_t2_ch1.czi │ │ ├── LLS7_t2_ch3.czi │ │ ├── RBC_lattice.tif │ │ ├── RBC_tiny.czi │ │ ├── README.txt │ │ ├── __init__.py │ │ ├── config │ │ │ ├── README.md │ │ │ ├── config.yaml │ │ │ └── config.yml │ │ ├── multich_multi_time.tif │ │ └── psfs │ │ │ └── zeiss_simulated │ │ │ ├── 488.czi │ │ │ ├── 488.tif │ │ │ ├── 561.czi │ │ │ ├── 561.tif │ │ │ ├── 640.czi │ │ │ ├── 640.tif │ │ │ ├── README.md │ │ │ └── description.txt │ ├── types.py │ ├── utils.py │ ├── workflow.py │ └── writers.py ├── pyproject.toml └── tests │ ├── __init__.py │ ├── conftest.py │ ├── data │ ├── crop │ │ ├── roi_1.tif │ │ ├── roi_2.tif │ │ └── two_rois.zip │ ├── deconvolved.tif │ ├── psf.tif │ └── raw.tif │ ├── params.py │ ├── test_arg_parser.py │ ├── test_cli.py │ ├── test_crop_deskew.py │ ├── test_deconvolution.py │ ├── test_deskew.py │ ├── test_process.py │ ├── test_validation.py │ ├── test_workflows.py │ ├── utils.py │ └── workflows │ ├── argument_order │ ├── custom_function.py │ └── test_workflow.yml │ └── binarisation │ └── workflow.yml ├── deploy.bat ├── docs ├── api.md ├── cli.md ├── deskew.png ├── development.md ├── files │ └── zeiss_lls7_MIP_rotate_roi.ijm ├── images │ ├── 001_start_plugin.png │ ├── 002_plugin.png │ ├── 003_open_image.png │ ├── 004_configure.png │ ├── 005_deskewed.png │ ├── 006_quick_deskew_checkbox.png │ ├── 007_quick_deskew_active.png │ ├── 008_deconvolution_tab.png │ ├── 009_deconvolution_options.png │ ├── 010_deconvolution_executed.png │ ├── 011_crop_tick.png │ ├── 012_crop_layer_roi.png │ ├── 013_crop_draw_roi.png │ ├── 014_crop_draw_roi_multiple.png │ ├── 015_crop_napari_layer.png │ ├── crop_fiji │ │ └── 001_fiji_rotate.png │ ├── deskew_active.png │ ├── green_tick.png │ ├── miscellaneous │ │ ├── 001_mips_bioformats.png │ │ ├── 002_MIPS_Annotate.png │ │ ├── 003_macro_window.png │ │ └── 004_enter_series.png │ ├── plugin_tabs.png │ └── video │ │ └── quick_deskew_timeseries.mp4 ├── index.md ├── installation.md ├── miscellaneous │ ├── index.md │ └── rois_cropping.md ├── napari_plugin │ ├── index.md │ ├── plugin_usage.md │ └── starting_plugin.md └── workflows │ ├── img │ ├── 1_gaussian.png │ ├── 2_otsu.png │ ├── 3_labelling.png │ └── 4_workflow_inspector.png │ ├── index.md │ ├── interactive_workflow.md │ ├── notebooks │ ├── Image_analysis_workflow_advanced.ipynb │ └── Image_analysis_workflow_simple.ipynb │ └── programmatic_workflow.md ├── mkdocs.yml ├── notebooks ├── Deskew_Save.ipynb ├── README.md ├── educational │ ├── deskew_artefact_opm_comparison.ipynb │ ├── deskewing_demo_pyclesperanto_prototype.ipynb │ └── inverse_deskewing_and_crop_deskew.ipynb ├── old │ ├── Using workflows in functions.ipynb │ ├── deconvolution_RedFishLion_1 LMAP.ipynb │ ├── deconvolution_RedLionFish.ipynb │ ├── deconvolution_pycudadecon.ipynb │ ├── psf_cropping.ipynb │ ├── save_bigdataviewer_h5_affine_transform.ipynb │ ├── saving_images_tiffile.ipynb │ └── tiling_images.ipynb └── troubleshooting │ └── troubleshooting_workflows.ipynb ├── plugin ├── napari_lattice │ ├── circle-regular.svg │ ├── disableable.py │ ├── dock_widget.py │ ├── fields.py │ ├── green.png │ ├── grey.png │ ├── icons.py │ ├── invalid.svg │ ├── napari.yaml │ ├── parent_connect.py │ ├── reader.py │ ├── red.png │ ├── shape_selection.py │ ├── shape_selector.py │ ├── utils.py │ └── valid.svg ├── pyproject.toml └── tests │ └── test_dock_widget.py ├── resources ├── cropping │ └── cropping_explanation.jpg ├── initialize │ ├── 0_init_plugin.jpg │ ├── 1_init_options.jpg │ ├── 2_last_dim.jpg │ └── 3_choose_device.jpg ├── misc │ ├── download_files_github.jpg │ ├── save_config_right_click_file.png │ └── save_config_right_click_raw.png └── workflows │ ├── 10_overview.jpg │ ├── 11_save_load_workflow.jpg │ ├── 12_workflow1.jpg │ ├── 13_workflow_preview.jpg │ ├── 14_workflow_crop_1.jpg │ ├── 14_workflow_crop_2.jpg │ ├── 15_workflow_save.jpg │ ├── 16_workflow_complete.jpg │ ├── 1_pyclesp_asst.jpg │ ├── 2_float_panel.jpg │ ├── 3_gaussian_blur.jpg │ ├── 4_threshold.jpg │ ├── 5_threshold.jpg │ ├── 6_labelling.jpg │ ├── 7_workflow_inspector.jpg │ ├── 8_voronoi_otsu.jpg │ ├── 9_workflow_inspector.jpg │ ├── custom_workflows │ ├── cellpose1_workflow.jpg │ └── regionprops_workflow1.jpg │ └── workflow_overview.jpg ├── sample_data ├── README.md └── roi_correct_zeiss_lls7.ijm ├── tox.ini └── workflow_examples ├── RBC_lattice.tif ├── cellpose ├── cellpose_1.py ├── 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