|Author||Seth Winfree ()|
|Maintainer||Seth Winfree ()|
|Development status||v0.3.7, beta|
Volumetric Tissue Exploration and Analysis
We developed VTEA out of a need to unify the various tasks involved in image processing, segmenting, exploring and analyzing large 3D fluorescence light microscopy image volumes ranging from 50-100s of microns thick. Our solution is predicated upon the idea that image processing, segmentation and analysis of 3D image volumes is best implemented with a bidirectional interactive user interface from image processing to analysis.
Importantly, our solution is in its infancy. In fact, the tools are relatively simple ones drawn from ImageJ's core functions. These first tools represent only the beginning of our vision for VTEA. We are currently planning to leverage the SciJava framework to make VTEA easily extensible and continue to build both upon existing tools in ImageJ/Fiji and our own novel approaches.
To install the VTEA plugin use, How to follow a 3rd party update site and check the update site: "Volumetric Tissue Exploration and Analysis" OR follow the following four steps:
1. Start updater
Select "Update..." under "Help".
2. Add update site
Select "Manage update sites."
3. Select update site
Check "Volumetric Tissue Expl..." and select "Close"
4. Apply changes
Select "Apply changes". Upon restart, the plugin will be present under a new menu "IU_Tools".
The utility of VTEA and 3D tissue cytometry was demonstrated in the following publication:
Quantitative Three-Dimensional Tissue Cytometry to Study Kidney Tissue and Resident Immune Cells Seth Winfree, Shehnaz Khan, Radmila Micanovic, Michael T. Eadon, Katherine J. Kelly, Timothy A. Sutton, Carrie L. Phillips, Kenneth W. Dunn, and Tarek M. El-Achkar JASN ASN.2016091027; published ahead of print February 2, 2017, doi:10.1681/ASN.2016091027