├── .github └── workflows │ └── book.yml ├── .gitignore ├── LICENSE-CC-BY ├── ObjectClassifier.cl ├── README.md ├── clean.sh ├── data ├── Haase_MRT_tfl3d1.tif ├── IXMtest_A02_s9.tif ├── IXMtest_A02_s9_image_data_source.txt └── blobs.tif ├── docs ├── 00_course_preparation │ ├── Readme.md │ └── img.png ├── 10_Clesperanto │ ├── 10_select_devices.ipynb │ ├── 20_gpu_arrays_and_memory_managment.ipynb │ ├── 30_apply_operations_on_data.ipynb │ ├── 40_nuclei_segmentation.ipynb │ ├── 50_measurement_and_quantifications.ipynb │ ├── 60_custom_kernel_execution.ipynb │ ├── 70_benchmarking.ipynb │ ├── clesperanto-polbias-course.pdf │ ├── maximum_z_projection.cl │ └── readme.md ├── 23_clesperanto_assistant │ ├── Intro_Napari_Assistant.pdf │ ├── images │ │ ├── export_notebooks.mp4 │ │ ├── export_notebooks01.jpg │ │ ├── export_notebooks02.jpg │ │ ├── export_notebooks03.jpg │ │ ├── export_notebooks04.jpg │ │ ├── export_notebooks05.jpg │ │ ├── export_notebooks06.jpg │ │ ├── export_notebooks07.jpg │ │ ├── export_notebooks08.jpg │ │ ├── export_notebooks09.jpg │ │ ├── filter_clesperanto.png │ │ ├── hela_cells_screenshot.png │ │ ├── install_package01.png │ │ ├── napari-assistant.mp4 │ │ ├── napari-assistant01.jpg │ │ ├── napari-assistant02.jpg │ │ ├── napari-assistant03.jpg │ │ ├── napari-assistant04.jpg │ │ ├── napari-assistant05.jpg │ │ ├── napari-assistant06.jpg │ │ ├── napari-assistant07.jpg │ │ ├── napari-assistant08.jpg │ │ ├── napari-assistant09.jpg │ │ ├── napari-assistant10.jpg │ │ ├── napari-assistant11.jpg │ │ ├── napari-assistant12.jpg │ │ ├── napari-assistant13.jpg │ │ ├── napari-assistant14.jpg │ │ ├── napari-assistant15.jpg │ │ ├── napari-assistant16.jpg │ │ ├── napari-assistant17.jpg │ │ ├── napari-assistant18.jpg │ │ └── napari-assistant1_.jpg │ ├── intro.md │ ├── napari-assistant.md │ └── notebook_export.md ├── 25_cupy │ ├── 10_basics.ipynb │ ├── 20_dropin_replacement.ipynb │ ├── 30_filtering.ipynb │ ├── 40_custom_kernels.ipynb │ ├── 50_napari-cupy-image-processing.ipynb │ ├── 60_benchmark_affine_transforms.ipynb │ ├── colab_runtime.png │ ├── cupy.pdf │ ├── napari-assistant-cupy.png │ ├── napari-assistant-generated-cupy-notebook.ipynb │ └── readme.md ├── 30_Deconvolution │ ├── 0_intro_to_decon.md │ ├── 10_decon_systems_design.ipynb │ ├── 1_test_libs.ipynb │ ├── 2_cupy_forward.ipynb │ ├── 3_Nuclei_Deconvolution_Compare_to_Truth.ipynb │ ├── 4_Nuclei_Deconvolution_Segmentation.ipynb │ ├── 5_edges.ipynb │ ├── 6_decon_bead_edge_handling.ipynb │ ├── 7_decon_regularization.ipynb │ ├── 8_extract_psf.ipynb │ ├── 9_Dask_Deconvolution.ipynb │ ├── cluster_access.md │ ├── decon_helper.py │ ├── images │ │ ├── 5_open_terminal.png │ │ ├── 6_terminal_output.png │ │ ├── 8_select_kernel.png │ │ ├── PSF_xy.jpg │ │ ├── PSF_xz.jpg │ │ ├── rl_iterations │ │ │ ├── rl10xy.jpg │ │ │ ├── rl10xz.jpg │ │ │ ├── rl20xy.jpg │ │ │ ├── rl20xz.jpg │ │ │ ├── rl30xy.jpg │ │ │ ├── rl30xz.jpg │ │ │ ├── xy.jpg │ │ │ └── xz.jpg │ │ ├── rl_rltv │ │ │ ├── sphere_deconvolved_rla50_xy.jpg │ │ │ ├── sphere_deconvolved_rla50_xz.jpg │ │ │ ├── sphere_deconvolved_rltv0.002_a50_xy.jpg │ │ │ └── sphere_deconvolved_rltv0.002_a50_xz.jpg │ │ ├── sphere_convolved_noise_xy.jpg │ │ ├── sphere_convolved_noise_xz.jpg │ │ ├── sphere_convolved_xy.jpg │ │ ├── sphere_convolved_xz.jpg │ │ ├── sphere_xy.jpg │ │ └── sphere_xz.jpg │ ├── labels_decon1.png │ ├── labels_decon2.png │ ├── labels_im.png │ ├── test.png │ └── test_libs.py ├── 40_HPC_Intro │ ├── Intro_to_HPC_POLBIAS_Handout.pdf │ ├── data │ │ ├── myscript.py │ │ ├── myscript.sbatch │ │ └── requirements.txt │ └── readme.md ├── 50_Clesperanto_on_HPC │ ├── exercises.md │ ├── images │ │ ├── 5_open_terminal.png │ │ ├── 6_terminal_output.png │ │ ├── taurus_login.png │ │ ├── taurus_login_1.png │ │ ├── taurus_login_2.png │ │ ├── taurus_login_3.png │ │ ├── taurus_login_4.png │ │ ├── taurus_login_6.png │ │ └── taurus_login_7.png │ ├── login_taurus.md │ ├── modified_generated_notebook.ipynb │ ├── napari_assistant_generated_notebook.ipynb │ └── readme.md ├── 60_Pytorch │ ├── 00_versions.ipynb │ ├── 01_data_exploration.ipynb │ ├── 02_dataset.ipynb │ ├── 03_data_batching_and_setup_model.ipynb │ ├── 04_model_training.ipynb │ ├── 05_model_training_with_device.ipynb │ ├── 06_model_training_with_logging.ipynb │ ├── 07_model_training_with_checkpoints.ipynb │ ├── 08_pytorch_lightning.ipynb │ ├── data.py │ ├── enable_env_in_jupyter.sh │ ├── readme.md │ ├── requirements.txt │ └── unet.png ├── 70_AI_Segmentation_Denoising │ ├── 01_2D_unet_training.ipynb │ ├── 02_Noise2Void.ipynb │ ├── 03_Noise2Void_3D.ipynb │ ├── CNNs_N2V.pdf │ ├── HPC_settings.PNG │ ├── Readme.md │ └── models │ │ └── n2v_3D │ │ └── logs │ │ └── images │ │ └── .nfs0000000005caaf5600000072 ├── 80_image_analysis_with_dask │ ├── 1_dask_basics.ipynb │ ├── 202308_dask_workshop_slides.pdf │ ├── 2_dask_image.ipynb │ ├── 3_lazy_image_processing.ipynb │ ├── README.md │ ├── dask-array.svg │ ├── dask-overview.svg │ ├── environment.yml │ ├── mydask.html │ └── mydask.png ├── 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