├── .coveragerc ├── .github └── workflows │ ├── publish_docs.yml │ └── pull_requests.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CITATION.cff ├── LICENSE.txt ├── README.md ├── dexp ├── __init__.py ├── cli │ ├── __init__.py │ ├── config.py │ ├── defaults.py │ ├── dexp_commands │ │ ├── __init__.py │ │ ├── _test │ │ │ └── test_cli.py │ │ ├── add.py │ │ ├── background.py │ │ ├── check.py │ │ ├── copy.py │ │ ├── crop.py │ │ ├── deconv.py │ │ ├── denoise.py │ │ ├── deskew.py │ │ ├── extract_psf.py │ │ ├── fastcopy.py │ │ ├── fromraw.py │ │ ├── fuse.py │ │ ├── generic.py │ │ ├── histogram.py │ │ ├── info.py │ │ ├── projrender.py │ │ ├── register.py │ │ ├── segment.py │ │ ├── speedtest.py │ │ ├── stabilize.py │ │ ├── tiff.py │ │ └── view.py │ ├── dexp_main.py │ ├── install_main.py │ ├── parsing.py │ ├── video_commands │ │ ├── __init__.py │ │ ├── blend.py │ │ ├── mp4.py │ │ ├── overlay.py │ │ ├── resize.py │ │ ├── stack.py │ │ └── volrender.py │ └── video_main.py ├── conftest.py ├── datasets │ ├── __init__.py │ ├── _test │ │ ├── test_joined_dataset.py │ │ └── test_zarr_dataset.py │ ├── base_dataset.py │ ├── clearcontrol_dataset.py │ ├── demo │ │ └── demo_dataset.py │ ├── joined_dataset.py │ ├── ome_dataset.py │ ├── open_dataset.py │ ├── operations │ │ ├── __init__.py │ │ ├── _test │ │ │ ├── test_copy.py │ │ │ ├── test_deconv.py │ │ │ ├── test_denoise.py │ │ │ ├── test_deskew.py │ │ │ ├── test_projrender.py │ │ │ ├── test_segment.py │ │ │ ├── test_stabilize.py │ │ │ └── test_tiff.py │ │ ├── background.py │ │ ├── copy.py │ │ ├── crop.py │ │ ├── deconv.py │ │ ├── demo │ │ │ ├── demo_copy.py │ │ │ ├── demo_deconv.py │ │ │ ├── demo_deskew.py │ │ │ ├── demo_deskew_real.py │ │ │ ├── demo_projrender.py │ │ │ ├── demo_stabilize.py │ │ │ └── demo_tiff.py │ │ ├── denoise.py │ │ ├── deskew.py │ │ ├── extract_psf.py │ │ ├── fromraw.py │ │ ├── fuse.py │ │ ├── generic.py │ │ ├── histogram.py │ │ ├── projrender.py │ │ ├── register.py │ │ ├── segment.py │ │ ├── stabilize.py │ │ ├── tiff.py │ │ └── view.py │ ├── stack_iterator.py │ ├── synthetic_datasets │ │ ├── __init__.py │ │ ├── _test │ │ │ ├── test_binary_blobs.py │ │ │ ├── test_multiview_data.py │ │ │ └── test_nuclei_background_data.py │ │ ├── binary_blobs.py │ │ ├── demo │ │ │ ├── demo_binary_blobs.py │ │ │ ├── demo_multiview_data.py │ │ │ └── demo_nuclei_background_data.py │ │ ├── dexp_dataset.py │ │ ├── multiview_data.py │ │ └── nuclei_background_data.py │ ├── tiff_dataset.py │ └── zarr_dataset.py ├── io │ ├── __init__.py │ ├── _test │ │ └── test_compress_array.py │ ├── compress_array.py │ └── io.py ├── optics │ ├── __init__.py │ └── psf │ │ ├── LICENSE.txt │ │ ├── __init__.py │ │ ├── _test │ │ └── test.py │ │ ├── demo │ │ └── demo.py │ │ ├── microscope_psf.py │ │ └── standard_psfs.py ├── processing │ ├── __init__.py │ ├── color │ │ ├── __init__.py │ │ ├── _test │ │ │ ├── test_blend.py │ │ │ ├── test_border.py │ │ │ ├── test_colormap.py │ │ │ ├── test_crop_resize_pad.py │ │ │ ├── test_insert.py │ │ │ ├── test_projection.py │ │ │ ├── test_scale_bar.py │ │ │ └── test_time_stamp.py │ │ ├── blend.py │ │ ├── border.py │ │ ├── cairo_utils.py │ │ ├── colormap.py │ │ ├── conversions.py │ │ ├── crop_resize_pad.py │ │ ├── demo │ │ │ ├── demo_blend.py │ │ │ ├── demo_border.py │ │ │ ├── demo_colormap.py │ │ │ ├── demo_crop_resize_pad.py │ │ │ ├── demo_insert.py │ │ │ ├── demo_projection.py │ │ │ ├── demo_scale_bar.py │ │ │ └── demo_time_stamp.py │ │ ├── insert.py │ │ ├── projection.py │ │ ├── projection_legend.py │ │ ├── scale_bar.py │ │ └── time_stamp.py │ ├── crop │ │ ├── __init__.py │ │ ├── _test │ │ │ ├── __init__.py │ │ │ └── test_rep_crop.py │ │ ├── background.py │ │ ├── demo │ │ │ ├── __init__.py │ │ │ └── demo_rep_crop.py │ │ └── representative_crop.py │ ├── deconvolution │ │ ├── __init__.py │ │ ├── _test │ │ │ ├── test_admm_deconvolution.py │ │ │ ├── test_admm_utils.py │ │ │ └── test_lr_deconvolution.py │ │ ├── admm_deconvolution.py │ │ ├── admm_utils.py │ │ ├── blind_deconvolution.py │ │ ├── demo │ │ │ ├── demo_admm_deconvolution_3d.py │ │ │ ├── demo_blind_deconv_3d.py │ │ │ ├── demo_inversion_deconvolution_3d.py │ │ │ ├── demo_lr_deconvolution_2d.py │ │ │ ├── demo_lr_deconvolution_2d_bs.py │ │ │ ├── demo_lr_deconvolution_2d_wb.py │ │ │ ├── demo_lr_deconvolution_3d.py │ │ │ ├── demo_lr_deconvolution_3d_bs.py │ │ │ ├── demo_lr_deconvolution_3d_sg.py │ │ │ └── demo_lr_deconvolution_3d_wb.py │ │ ├── inversion_deconvolution.py │ │ └── lr_deconvolution.py │ ├── denoising │ │ ├── __init__.py │ │ ├── _test │ │ │ ├── __init__.py │ │ │ ├── test_butterworth.py │ │ │ ├── test_gaussian.py │ │ │ └── test_noise.py │ │ ├── butterworth.py │ │ ├── demo │ │ │ ├── __init__.py │ │ │ ├── demo_2D_butterworth.py │ │ │ ├── demo_2D_gaussian.py │ │ │ ├── demo_3D_butterworth.py │ │ │ └── demo_noise.py │ │ ├── gaussian.py │ │ ├── j_invariance.py │ │ ├── metrics.py │ │ └── noise.py │ ├── deskew │ │ ├── __init__.py │ │ ├── _test │ │ │ ├── test_classic_deskew.py │ │ │ └── test_yang_deskew.py │ │ ├── classic_deskew.py │ │ ├── demo │ │ │ ├── demo_classic_deskew.py │ │ │ └── demo_yang_deskew.py │ │ ├── utils.py │ │ └── yang_deskew.py │ ├── equalise │ │ ├── __init__.py │ │ ├── _test │ │ │ └── test_equalise_intensity.py │ │ ├── demo │ │ │ └── demo_equalise_intensity.py │ │ └── equalise_intensity.py │ ├── filters │ │ ├── __init__.py │ │ ├── _test │ │ │ ├── test_butterworth.py │ │ │ ├── test_fft_convolve.py │ │ │ └── test_sobel.py │ │ ├── butterworth_filter.py │ │ ├── demo │ │ │ ├── demo_butterworth_filter.py │ │ │ ├── demo_fft_convolve.py │ │ │ └── demo_sobel.py │ │ ├── fft_convolve.py │ │ ├── kernels │ │ │ ├── __init__.py │ │ │ ├── _test │ │ │ │ └── test_gaussian.py │ │ │ ├── butterworth.py │ │ │ ├── demo │ │ │ │ ├── demo_butterworth.py │ │ │ │ ├── demo_gaussian.py │ │ │ │ ├── demo_wiener.py │ │ │ │ └── demo_wiener_butterworth.py │ │ │ ├── gaussian.py │ │ │ ├── wiener.py │ │ │ └── wiener_butterworth.py │ │ └── sobel_filter.py │ ├── fusion │ │ ├── __init__.py │ │ ├── _test │ │ │ ├── test_dct_fusion.py │ │ │ ├── test_dft_fusion.py │ │ │ └── test_tg_fusion.py │ │ ├── dct_fusion.py │ │ ├── demo │ │ │ └── demo_fusion.py │ │ ├── dft_fusion.py │ │ └── tg_fusion.py │ ├── interpolation │ │ ├── __init__.py │ │ ├── _cupy │ │ │ ├── __init__.py │ │ │ ├── warp_1d.py │ │ │ ├── warp_2d.py │ │ │ └── warp_3d.py │ │ ├── _test │ │ │ ├── test_warp_1d.py │ │ │ ├── test_warp_2d.py │ │ │ └── test_warp_3d.py │ │ ├── demo │ │ │ ├── demo_warp_1d.py │ │ │ ├── demo_warp_2d.py │ │ │ └── demo_warp_3d.py │ │ └── warp.py │ ├── morphology │ │ ├── __init__.py │ │ ├── _test │ │ │ └── test_componet_tree.py │ │ ├── component_tree.py │ │ └── utils.py │ ├── multiview_lightsheet │ │ ├── __init__.py │ │ ├── deconvolution │ │ │ ├── __init__.py │ │ │ └── demo │ │ │ │ └── demo_simview_deconv.py │ │ └── fusion │ │ │ ├── __init__.py │ │ │ ├── basefusion.py │ │ │ ├── demo │ │ │ ├── demo_mvsols_fusion.py │ │ │ └── demo_simview_fusion.py │ │ │ ├── mvsols.py │ │ │ └── simview.py │ ├── optimization │ │ ├── __init__.py │ │ ├── demo │ │ │ └── demo_grid_search_admm_deconv_3d.py │ │ └── grid_search.py │ ├── registration │ │ ├── __init__.py │ │ ├── _test │ │ │ ├── test_register_warp_2d.py │ │ │ ├── test_register_warp_3d.py │ │ │ ├── test_sequence_2d.py │ │ │ ├── test_sequence_3d.py │ │ │ ├── test_translation_2d.py │ │ │ ├── test_translation_3d.py │ │ │ ├── test_translation_3d_maxproj.py │ │ │ ├── test_translation_3d_maxproj_difficult.py │ │ │ ├── test_translation_nd.py │ │ │ ├── test_warp_2d_blobs.py │ │ │ ├── test_warp_ms_2d.py │ │ │ └── test_warp_ms_3d.py │ │ ├── demo │ │ │ ├── demo_sequence_2d.py │ │ │ ├── demo_sequence_3d.py │ │ │ ├── demo_translation_2d.py │ │ │ ├── demo_translation_3d.py │ │ │ ├── demo_translation_3d_proj.py │ │ │ ├── demo_translation_3d_proj_difficult.py │ │ │ ├── demo_warp_2d.py │ │ │ ├── demo_warp_2d_blobs.py │ │ │ ├── demo_warp_3d.py │ │ │ ├── demo_warp_ms_2d.py │ │ │ └── demo_warp_ms_3d.py │ │ ├── model │ │ │ ├── __init__.py │ │ │ ├── _test │ │ │ │ ├── test_model_io.py │ │ │ │ ├── test_sequence_model.py │ │ │ │ ├── test_translation_model.py │ │ │ │ └── test_warp_model.py │ │ │ ├── demo │ │ │ │ ├── demo_translation_model.py │ │ │ │ └── demo_warp_model.py │ │ │ ├── model_io.py │ │ │ ├── pairwise_registration_model.py │ │ │ ├── sequence_registration_model.py │ │ │ ├── translation_registration_model.py │ │ │ └── warp_registration_model.py │ │ ├── sequence.py │ │ ├── sequence_proj.py │ │ ├── translation_2d.py │ │ ├── translation_nd.py │ │ ├── translation_nd_proj.py │ │ ├── warp_multiscale_nd.py │ │ └── warp_nd.py │ ├── remove_beads │ │ ├── __init__.py │ │ ├── beadsremover.py │ │ └── demo │ │ │ └── demo_remove_beads.py │ ├── restoration │ │ ├── __init__.py │ │ ├── _test │ │ │ ├── test_aap_correction.py │ │ │ ├── test_clean_dark_regions.py │ │ │ ├── test_dehaze.py │ │ │ └── test_lipschitz_continuity_correction.py │ │ ├── aap_correction.py │ │ ├── clean_dark_regions.py │ │ ├── dehazing.py │ │ ├── demo │ │ │ ├── demo_aap_correction.py │ │ │ ├── demo_clean_dark_regions.py │ │ │ ├── demo_dehaze.py │ │ │ └── demo_lipschitz_continuity_correction.py │ │ └── lipshitz_correction.py │ ├── segmentation │ │ ├── __init__.py │ │ └── watershed.py │ └── utils │ │ ├── __init__.py │ │ ├── _test │ │ ├── test_blend_images.py │ │ ├── test_center_of_mass.py │ │ ├── test_element_wise_affine.py │ │ ├── test_fit_shape.py │ │ ├── test_linear_solver.py │ │ ├── test_nan_to_zero.py │ │ ├── test_normalise.py │ │ ├── test_projection_generator.py │ │ ├── test_scatter_gather_i2i.py │ │ └── test_scatter_gather_i2v.py │ │ ├── apply.py │ │ ├── blend_images.py │ │ ├── center_of_mass.py │ │ ├── element_wise_affine.py │ │ ├── fit_shape.py │ │ ├── linear_solver.py │ │ ├── mkl_util.py │ │ ├── nan_to_zero.py │ │ ├── nd_slice.py │ │ ├── normalise.py │ │ ├── pad.py │ │ ├── projection_generator.py │ │ ├── scatter_gather_i2i.py │ │ └── scatter_gather_i2v.py ├── utils │ ├── __init__.py │ ├── _test │ │ └── test_speed_test.py │ ├── backends │ │ ├── __init__.py │ │ ├── _cupy │ │ │ ├── __init__.py │ │ │ └── texture │ │ │ │ ├── __init__.py │ │ │ │ ├── _test │ │ │ │ └── test_texture.py │ │ │ │ └── texture.py │ │ ├── _test │ │ │ ├── test_backend.py │ │ │ ├── test_cupy_backend.py │ │ │ └── test_numpy_backend.py │ │ ├── backend.py │ │ ├── best_backend.py │ │ ├── cupy_backend.py │ │ └── numpy_backend.py │ ├── config.py │ ├── dask.py │ ├── fft.py │ ├── lock.py │ ├── misc.py │ ├── robocopy.py │ ├── slicing.py │ ├── speed_test.py │ ├── testing │ │ ├── __init__.py │ │ └── testing.py │ └── timeit.py ├── video │ ├── __init__.py │ ├── _test │ │ ├── test_overlay.py │ │ ├── test_video_blend.py │ │ └── test_video_crop_resize_pad.py │ ├── blend.py │ ├── crop_resize_pad.py │ ├── demo │ │ ├── demo_blend.py │ │ ├── demo_crop_resize_pad.py │ │ └── demo_overlay.py │ └── overlay.py └── volumerender │ ├── __init__.py │ ├── demo │ └── demo_volumerender.py │ ├── kernels │ ├── all_render_kernels.cl │ ├── convolve_2d.cl │ ├── iso_kernel.cl │ ├── iso_kernel_tmp.cl │ ├── occlusion.cl │ ├── utils.cl │ └── volume_kernel.cl │ ├── quaternion.py │ ├── transform_matrices.py │ └── volumerender.py ├── docs ├── .nojekyll ├── Makefile ├── README.md ├── _templates │ └── autosummary │ │ └── module.rst ├── index.html ├── make.bat ├── requirements-docs.txt └── source │ ├── api │ └── api.rst │ ├── commands │ ├── dexp_commands.rst │ └── video_commands.rst │ ├── conf.py │ ├── getting_started │ ├── contact_us.rst │ └── install.rst │ ├── how_to_guides │ ├── data_conversion.md │ ├── data_conversion.py │ ├── implementing_processing.md │ ├── implementing_processing.py │ ├── processing_multi_view.md │ └── visualization.md │ └── index.rst ├── env-linux-gpu.yaml ├── install_linux_ppc.sh ├── pyproject.toml └── setup.py /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/royerlab/dexp/HEAD/.coveragerc -------------------------------------------------------------------------------- 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