Organ Inserter Step

Overview

The Organ Inserter step is an interactive plugin for the MAP-Client.

The Organ Inserter currently inserts organ scaffold in the whole body scaffold via one of the three available modes: common trunk, pass through and default.

The common trunk mode adopts a trunk from a template scaffold file and uses the path of the template trunk to determine the path of the branches of an organ scaffold. The template scaffold has to be derived from the same subject from which the whole body scaffold was generated from. This mode is currently used for inserting subject-specific vagus scaffolds. It can potentially be used in future for handling airways, circulatory systems or other nerves.

The pass through mode handles organ scaffolds that have already been built or are derived from the same subject as the whole body scaffold. They should already be in the same coordinate system as the whole body scaffold and will not require any further processing for organ insertion, hence these scaffold files will be passed right through. Currently used for gastrointestinal tract, diaphragm, bone, muscle, arteries and veins.

The default mode performs a rigid body transformation to align fiducial markers in the organ scaffold to the same markers present in the whole body scaffold in order to achieve organ insertion. This mode will require at least 3 non-collinear markers for each organ to work. This is currently used for inserting the brainstem, heart, lungs and bladder.

This tool takes a Zinc compatible whole body scaffold EX file as a first input, one or more Zinc compatible organ scaffold EX file as a second input and one or more Zinc compatible template organ scaffold EX file as an optional third input. The Organ Inserter step outputs a series of Zinc compatible EX files of the organ scaffolds with coordinates transformed to the same coordinate system as the whole body scaffold, effectively resulting in the insertion of the organs in the whole body scaffold.

Specification

Information on this plugin’s specifications is available here.

Configuration

Information on this plugin’s configuration is available here.

Workflow Setup

Information on setting up a workflow with this plugin can be found here.

Instructions

This is a non-interactive step.