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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
Theme by the Executable Book Project
  • .md

Routines

RoutinesΒΆ

  • Preprocessing
  • Identification
  • Building chromatin traces
  • General-use scripts

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Overview

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Preprocessing

By Marcelo Nollmann, Xavier Devos
© Copyright 2022, Marcelo Nollmann, Xavier Devos.