VTEA

Revision as of 17:25, 25 March 2017 by ICBM-IUPUI (talk | contribs) (TODO: added to todo)

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vtea_ (Fiji)
Author Seth Winfree ([1])
Maintainer Seth Winfree ([2])
Source on GitHub
Development status v0.3.7, beta
Category Segmentation,Visualization,Plugins



Volumetric Tissue Exploration and Analysis



This brief video describes VTEA's core behaviors. VTEA's utility has been demonstrated in this paper.

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.


Installing

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".

Select "Update..." under "Help".

2. Add update site

Select "Manage update sites."

Select "Manage update sites."

3. Select update site

Check "Volumetric Tissue Expl..."

Check "Volumetric Tissue Expl..." and select "Close"

4. Apply changes

Check "Volumetric Tissue Expl..."

Select "Apply changes". Upon restart, the plugin will be present under a new menu "IU_Tools".

Tutorials

Image Processing

      Coming soon!

Segmentation

      Coming soon!

Analysis

      Coming soon!

Visualization

      Coming soon!

VTEA reference

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

TODO


TODO:
    1. add ground truth validation
    2. add workflow saving and export
    3. implement ImageFlow(http://imageflow.danielsenff.de) approach
    4. move out of development phase
    5. complete conversion to SciJava framework