VRL-Density-Vis

Introduction

The density visualization plugin is designed to analyze and visualize density distribution of proteins in neurons. But it can also be used for other types distributions.

The following section gives an overview over all provided components and their parameters.

Components

This plugin contains several components that can be combined into a complete workflow that computes and visualizes the density distribution and distances between voxel sets and the specified geometry.

Compute Density

This component divides the specified image stack into voxel sets and computes the average density in each set. Input and output parameters are shown in [Compute Density].

Compute Distances

This component computes the minimum distances between the center of each voxel set and the specified geometry. Input and output parameters are shown in [Compute Distances].

Density Visualization

This component visualizes the specified density information and the geometry. Input and output parameters are shown in [Density Visualization].

Visualizations can be saved as pixel image via Right-Click->Save Image. This is useful if the visualization shall be used in publications.

Histogram Plotter

This component creates a histogram plot of the specified distance data. Input and output parameters are shown in [Histogram Plotter].

INFO: currently disabled

The plot can be saved as vector image via Right-Click->Export. This is useful if the plot shall be used in publications.

How To Build The Plugin

1. Dependencies

• JDK >= 1.8 (tested with JDK 8-13)
• Internet Connection (other dependencies will be downloaded automatically)
• Optional: IDE with Gradle support

2. Configuration (Optional)

If the plugin shall be installed to a custom destination, specify the path in build.properties, e.g.,

# vrl property folder location (plugin destination)
vrldir=/path/to/.vrl/0.4.4/myvrl

Otherwise, the plugin will be installed to the default location (depends on VRL version that is specified in the gradle dependencies).

3. Build & Install

IDE

To build the project from an IDE do the following:

• open the Gradle project
• call the installVRLPlugin Gradle task to build and install the plugin
• restart VRL-Studio

Command Line

Building the project from the command line is also possible.

Navigate to the project folder and call the installVRLPlugin Gradle task to build and install the plugin.

Bash (Linux/OS X/Cygwin/other Unix-like OS)

cd Path/To/VRL-Density-Vis
bash ./gradlew installVRLPlugin

Windows (CMD)

cd Path\To\VRL-Density-Vis
gradlew installVRLPlugin

Finally, restart VRL-Studio