Image Pipe

Pipeline building solution for 4D biological microscopy

Description:

This project is still in development. Initially started as a tool for Ruan, Zhou et al, Nature 2017, this pipeline has since grown to allow arbitrary pipeline construction based on a set of primitive functions and abstractions (pipe, tiling, per-segment processing, etc…).

This project is currently in alpha development, hence poorly documented, sparsely tested and prone to rapid changes.

Basic installation:

> pip install imagepipe

or:

> pip install git+https://github.com/chiffa/Image_pipe.git

The documentation is available on readthedocs.

Project is housed at GitHub. For any issues please refer to GitHub issue tracker.

Usage Guides:

• Installation and requirements:
• Pipeline and functions overview:
• Basic usage:

Dev log:

• This is a general library for image processing
  • Logic in the
  • Desired code:
  • Remarks:
  • Formalism:
  • Sub-segmentation
  • Registering Run:
  • Possible usages:
  • Organization:
  • From the usage
  • Reformulation
  • Audit:

API documentation:

• imagepipe package
  • Subpackages
    • imagepipe.tools package
      • Submodules
      • imagepipe.tools.helpers module
      • Module contents
  • Submodules
  • imagepipe.core_functions module
  • imagepipe.debug_renders module
  • imagepipe.density_plot module
  • imagepipe.iterate_and_check_img_files module
  • imagepipe.raw_functions module
  • imagepipe.traversals module
  • imagepipe.wrapped_functions module
  • Module contents

Indices and tables

• Index
• Module Index
• Search Page