bunpc / vasculardataviz

Discription:

This app helps to visualize pO2pts, stalling segments on angiogram and get branch order statistics for that data.

input:

Angiogram volume
A file name is provided for a MAT or TIF file that contains the volumetric image of the angiogram. This is generally the angiogram image file and not a segmented angiogram.

Graph file
A file name is provided for a MAT file that contains the graph information with the following fields:
Graph.nodes [Nx3] - This is the 3D position of each of the N nodes in the graph
Graph.edges [Mx2] - This is the list of M edges giving the index for each of the 2 nodes connected by the given edge.
Graph.diam [Nx1] - This is the diameter at each node in units of micrometers.
Graph.nodeType [Nx1] - This indicates whether a node is an artery (1), a capillary (2), or a vein(3). This is optional in the input file.
Graph.segInfo - This is a data structure that contains information about the nodes and edges contained in each vascular segment.

OCT stall data
This is the output saved from capStallGUI.
The input has 5 variables:
Cap [Nx2] - contains 2D coordinates of the capillary stall points in the MIP coordinate system
Pts [Nx3] - contains 3D coordinates of the capillary stall points in the 3D average volume
Seg [Nx1]- is a structure data type.
Seg.pos [MX3]- contains positions of the capillary segment. Note that the number of node points M generally differs for each capillary segment.
Seg.mask [Px1] - contains a list of indices into the volume image indicating the voxels corresponding to the masked capillary segment.
Int_ts [NT] - contains the intensity time series of each segment averaged over the list of Seg.mask voxels for the given segment.
StallingMatrix [NT] - is binary matrix with stalls indicated as 1 and non-stalls as 0. This is the famous stall-o-gram.
N - number of stalling capillary segments
T - number of images in the time series

pO2 Data
This is pO2 points information pO2pts [Nx3] - contains 3D coordinates of pO2 pts in the measured volume.
N - number of po2 pts measured

Output:

Graph.pO2ptsBO -
Graph.IntrapO2ptspath -