LICENSE
README.md
pyproject.toml
pyhim.egg-info/PKG-INFO
pyhim.egg-info/SOURCES.txt
pyhim.egg-info/dependency_links.txt
pyhim.egg-info/entry_points.txt
pyhim.egg-info/requires.txt
pyhim.egg-info/top_level.txt
ressources/stardist_models/__init__.py
ressources/stardist_models/DAPI_2D_stardist_nc14_nrays64_epochs40_grid2/__init__.py
ressources/stardist_models/DAPI_2D_stardist_nc14_nrays64_epochs40_grid2/config.json
ressources/stardist_models/DAPI_2D_stardist_nc14_nrays64_epochs40_grid2/thresholds.json
ressources/stardist_models/DAPI_2D_stardist_nc14_nrays64_epochs40_grid2/weights_best.h5
ressources/stardist_models/DAPI_2D_stardist_nc14_nrays64_epochs40_grid2/weights_last.h5
ressources/stardist_models/DAPI_3D_stardist_17032021_deconvolved/__init__.py
ressources/stardist_models/DAPI_3D_stardist_17032021_deconvolved/config.json
ressources/stardist_models/DAPI_3D_stardist_17032021_deconvolved/thresholds.json
ressources/stardist_models/DAPI_3D_stardist_17032021_deconvolved/weights_best.h5
ressources/stardist_models/DAPI_3D_stardist_17032021_deconvolved/weights_last.h5
ressources/stardist_models/PSF_3D_stardist_20210618_simu_deconvolved_thresh_0_01/__init__.py
ressources/stardist_models/PSF_3D_stardist_20210618_simu_deconvolved_thresh_0_01/config.json
ressources/stardist_models/PSF_3D_stardist_20210618_simu_deconvolved_thresh_0_01/thresholds.json
ressources/stardist_models/PSF_3D_stardist_20210618_simu_deconvolved_thresh_0_01/weights_best.h5
ressources/stardist_models/PSF_3D_stardist_20210618_simu_deconvolved_thresh_0_01/weights_last.h5
src/core/__init__.py
src/core/dask_cluster.py
src/core/data_file.py
src/core/data_manager.py
src/core/function_caller.py
src/core/parameters.py
src/core/pyhim_logging.py
src/core/run_args.py
src/core/saving.py
src/imageProcessing/__init__.py
src/imageProcessing/alignImages.py
src/imageProcessing/alignImages3D.py
src/imageProcessing/imageProcessing.py
src/imageProcessing/localization_table.py
src/imageProcessing/localize_2d.py
src/imageProcessing/localize_3d.py
src/imageProcessing/makeProjections.py
src/imageProcessing/mask_2d.py
src/imageProcessing/mask_3d.py
src/imageProcessing/register_local.py
src/imageProcessing/segmentMasks.py
src/imageProcessing/segmentMasks3D.py
src/imageProcessing/segmentSources3D.py
src/matrixOperations/HIMmatrixOperations.py
src/matrixOperations/__init__.py
src/matrixOperations/build_matrix.py
src/matrixOperations/build_traces.py
src/matrixOperations/chromatin_trace_table.py
src/matrixOperations/filter_localizations.py
src/matrixOperations/register_localizations.py
src/plots/figure3wayInteractions.py
src/plots/figure4Mmatrix.py
src/plots/figureCompare2Matrices.py
src/plots/figureHiMmatrix.py
src/plots/figureN_HiMmatrices.py
src/plots/figureSingleCell.py
src/plots/plot_bootstrapping.py
src/plots/plotting_functions.py
src/postProcessing/analyze_localizations.py
src/postProcessing/compare_PWD_matrices.py
src/postProcessing/mask_cellpose.py
src/postProcessing/mask_manual.py
src/postProcessing/npy_to_tiff.py
src/postProcessing/processHiMmatrix.py
src/postProcessing/pwd_matrix_2_pdb.py
src/postProcessing/trace_analyzer.py
src/postProcessing/trace_assign_mask.py
src/postProcessing/trace_combinator.py
src/postProcessing/trace_filter.py
src/postProcessing/trace_filter_advanced.py
src/postProcessing/trace_merge.py
src/postProcessing/trace_plot.py
src/postProcessing/trace_to_matrix.py
src/toolbox/__init__.py
src/toolbox/imagePreProcessing.py
src/toolbox/imageSegmentSpots.py
src/toolbox/runHiM_cluster.py
src/toolbox/file_handling/cleanHiM_run.py
src/toolbox/file_handling/lndir.py
src/toolbox/file_handling/unzipHiM_run.py
src/toolbox/file_handling/zipHiM_run.py
src/toolbox/parameter_file/__init__.py
src/toolbox/parameter_file/function_parameters.py
src/toolbox/parameter_file/info_parameters.py
src/toolbox/parameter_file/parameters.json
src/toolbox/parameter_file/pyhim_image.png
src/toolbox/parameter_file/pyhim_parameters.py
tests/test_localize_2d.py
tests/test_localize_3d.py
tests/test_mask_2d.py
tests/test_projection.py
tests/test_pyhim.py
tests/test_register_global.py
tests/test_register_local.py