Welcome to plankton!

a python-based point process analysis package.

Plankton is a python package created to make data handling and analysis of point process data as easy as possible.

Introduction:

• Introduction
  • What are point processes?

Getting started

• Installation
• Tutorial 1: Data handling
  • Data Preparation
  • Creating a SpatialData object
  • Counts & statistics
  • Basic visualization
  • Spatial or not: Data Indexing
• Tutorial 2: Pixel map integration
  • Pixel maps as a plotting background
  • Parsing pixel map data
• Tutorial 3: Scanpy and AnnData integration
• Tutorial 4: Exploratory analysis
  • Recurring spatial contexts
• Tutorial 5: Statistical modeling

User guide:

• The SpatialData object:
• The PixelMap object
• The SpatialStatistics object
• Next Neighbor analysis and spatial contexts:
• Integrating scanpy/Anndata

Modules:

• plankton
  • plankton package
    • Submodules
    • plankton.graph module
    • plankton.pixelmaps module
    • plankton.plankton module
    • plankton.stats module
    • plankton.utils module
    • Module contents

Indices and tables

• Index

• Module Index

• Search Page