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CytoMAP
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Last edited by

DrStoltzfus Mar 02, 2021

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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