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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
.rst
.pdf
pyHiM main
pyHiM main
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