Difference between revisions of "Sprout Morphology"

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== Usage ==
 
== Usage ==
  
Open a maximum intensity projection of the multi-channel image to be analyzed, the start the plugin via {{bc|Analyze|Sprout Morphology}}. The process consists of up to six dialogs:
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Open a maximum intensity projection of the multi-channel image to be analyzed, then start the plugin via {{bc|Analyze|Sprout Morphology}}. The process consists of up to six dialogs:
  
 
=== General configuration ===
 
=== General configuration ===
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[[Image:SproutAnalyzer PericyteCoverage.png|400px|Pericyte coverage measurement]]
 
[[Image:SproutAnalyzer PericyteCoverage.png|400px|Pericyte coverage measurement]]
 
  
 
== Publication ==
 
== Publication ==

Revision as of 03:26, 18 January 2017

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, then 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

Publication