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Getting Started
Installation
Tutorials
Jupyter Notebook
pyHiM in 3D
Test installation
Parameters file
Cellpose for pyHiM
StarDist for pyHiM
Running pyHiM
User Guide
Introduction
Overview
Routines
Preprocessing
project
register_global
Apply registration
register_local
shift_mask
Identification
mask_2d and localize_2d
mask_3d
localize_3d
mask_manual
mask_cellpose
Building chromatin traces
filter_localizations
register_localizations
build_traces
build_matrices
General-use scripts
Reference
Use case diagrams
Parameters
API Reference
pyHiM main
core package
imageProcessing package
matrixOperations package
postProcessing package
toolbox package
toolbox.file_handling package
toolbox.parameter_file package
Contributor's Guide
Environment
Developer installation
Python coding style
Development process
Good practices before committing
How to document
No-python files
Reporting bugs and feature requests
How work with apiFISH
Additional resources
License
.md
.pdf
API Reference
API Reference
ΒΆ
pyHiM main
core package
Submodules
core.dask_cluster module
core.data_file module
core.data_manager module
core.function_caller module
core.parameters module
core.pyhim_logging module
core.run_args module
core.saving module
Module contents
imageProcessing package
Submodules
imageProcessing.alignImages module
imageProcessing.alignImages3D module
imageProcessing.imageProcessing module
imageProcessing.makeProjections module
imageProcessing.segmentMasks module
imageProcessing.segmentMasks3D module
imageProcessing.segmentSources3D module
Module contents
matrixOperations package
Submodules
matrixOperations.build_matrix_tempo module
matrixOperations.build_traces module
matrixOperations.filter_localizations module
matrixOperations.register_localizations module
Module contents
postProcessing package
Submodules
postProcessing.mask_cellpose module
postProcessing.mask_manual module
postProcessing.npy_to_tiff module
Module contents
toolbox package
Submodules
toolbox.imagePreProcessing module
toolbox.imageSegmentSpots module
Module contents
toolbox.file_handling package
Submodules
toolbox.file_handling.cleanHiM_run module
toolbox.file_handling.lndir module
toolbox.file_handling.unzipHiM_run module
toolbox.file_handling.zipHiM_run module
Module contents
toolbox.parameter_file package
Submodules
toolbox.parameter_file.function_parameters module
toolbox.parameter_file.info_parameters module
toolbox.parameter_file.pyhim_parameters module
Module contents
