Wiki Pages

CytoMAP

Introduction

Getting started with CytoMAP

  • Installation Guide
  • Main User Interface
  • Loading data

Visualizing Data

  • Visualize data with a new figure.
  • Smoothed Overlay
  • Defining Surfaces

Cellular Analysis

  • Calculating distance relationships
  • Clustering cells
  • Plot Sample Cellularity
  • Compare Cellular MFI

Neighborhood Analysis

  • Defining Neighborhoods
  • Define tissue regions using unsupervised clustering
  • Pseudospace
  • Cellular Correlations across neighborhoods

Region Analysis

  • Creating heatmaps of region composition
  • Region Statistics
  • Region Interactions
  • Edit Regions

Dimensionality Reduction

  • Overview
  • t-SNE
  • UMAP
  • PHATE
  • TSCAN
  • IOSMap
  • LLE
  • Examples

Extensions

  • Overview
  • Ripley Distribution Analysis
  • Compare Cells With Random Tree
  • Nearest Neighbor Analysis
  • Edit Figures Template
  • Edit All Figures Template
  • Calculate Dispersion
  • Bar and Violin Plots
  • Change Opacity
  • Overlay_Confocal_Images
  • Rotation Image

Examples

  • Basic Workflow
  • Clustering Cells