Difference between revisions of "Sprout Morphology"

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=== General configuration ===
 
=== General configuration ===
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[[Image:SproutAnalyzer Configuration.png|400px|Configuration dialog]]
  
 
=== Bead detection ===
 
=== Bead detection ===
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[[Image:SproutAnalyzer BeadDetection.png|400px|Bead detection]]
  
 
=== Sprout detection ===
 
=== Sprout detection ===
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[[Image:SproutAnalyzer SproutDetection.png|400px|Sprout detection]]
  
 
=== Nucleus segmentation ===
 
=== Nucleus segmentation ===
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[[Image:SproutAnalyzer NucleusSegmentation.png|400px|Nucleus segmentation]]
  
 
=== Endothelial cell/Pericyte classification ===
 
=== Endothelial cell/Pericyte classification ===
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[[Image:SproutAnalyzer CellClassification.png|400px|Cell classification of ECs and pericytes]]
  
 
=== Pericyte coverage ===
 
=== Pericyte coverage ===
  
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[[Image:SproutAnalyzer PericyteCoverage.png|400px|Pericyte coverage measurement]]
  
  
 
== Citation ==
 
== Citation ==

Revision as of 15:52, 10 July 2016

Sprout Morphology (Fiji)
Author Jan Eglinger
Maintainer Jan Eglinger
Source on GitHub
Development status stable
Category Analysis


The Sprout Morphology plugin measures sprout number, length, width and cell density of endothelial cell (EC) sprouts grown in a bead sprouting assay. It optionally includes measuring the coverage of these sprouts with pericytes included in the assay, as well as the endothelial cell/pericyte ratio.

Installation

To install the plugin, activate the Angiogenesis update site and restart Fiji.

Usage

Open a maximum intensity projection of the multi-channel image to be analyzed, the start the plugin via Analyze › Sprout Morphology. The process consists of up to six dialogs:

General configuration

Configuration dialog

Bead detection

Bead detection

Sprout detection

Sprout detection

Nucleus segmentation

Nucleus segmentation

Endothelial cell/Pericyte classification

Cell classification of ECs and pericytes

Pericyte coverage

Pericyte coverage measurement


Citation