LICENSE
README.md
pyproject.toml
src/pyHiM.py
src/fileProcessing/__init__.py
src/fileProcessing/changeRT_infoList.py
src/fileProcessing/cleanHiM_run.py
src/fileProcessing/fileManagement.py
src/fileProcessing/functionCaller.py
src/fileProcessing/lndir.py
src/fileProcessing/runHiM_cluster.py
src/fileProcessing/unzipHiM_run.py
src/fileProcessing/zipHiM_run.py
src/imageProcessing/__init__.py
src/imageProcessing/alignImages.py
src/imageProcessing/alignImages3D.py
src/imageProcessing/imagePreProcessing.py
src/imageProcessing/imageProcessing.py
src/imageProcessing/imageSegmentSpots.py
src/imageProcessing/localization_table.py
src/imageProcessing/makeProjections.py
src/imageProcessing/segmentMasks.py
src/imageProcessing/segmentMasks3D.py
src/imageProcessing/segmentSources3D.py
src/matrixOperations/HIMmatrixOperations.py
src/matrixOperations/__init__.py
src/matrixOperations/alignBarcodesMasks.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/parameter_file/__init__.py
src/parameter_file/function_parameters.py
src/parameter_file/infoList.json
src/parameter_file/infoList_mesoLR.json
src/parameter_file/infoList_model.json
src/parameter_file/info_parameters.py
src/parameter_file/pyhim_image.png
src/parameter_file/pyhim_parameters.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/postProcessing/npy_to_tiff.py
src/postProcessing/processHiMmatrix.py
src/postProcessing/processSNDchannel.py
src/postProcessing/process_segmentMasks3D.py
src/postProcessing/trace_analyzer.py
src/postProcessing/trace_combinator.py
src/postProcessing/trace_filter.py
src/postProcessing/trace_selector.py
src/pyhim.egg-info/PKG-INFO
src/pyhim.egg-info/SOURCES.txt
src/pyhim.egg-info/dependency_links.txt
src/pyhim.egg-info/entry_points.txt
src/pyhim.egg-info/requires.txt
src/pyhim.egg-info/top_level.txt