V2.1.0

Summer 2023 version

Used in the stroke model study publication [1]

Additional and improved visualization methods:

1. custom 3D rendering with control over color-coding e.g. directional coloring
2. built-in ROI selection during final analysis step for sub-sampling and investigating

Added support for training and deploying a machine learner (in python) on the task of manual vertex curation.

[1]

@article{mihelic2023microvascular,
  title={Microvascular plasticity in stroke recovery: Longitudinal snapshots, network statistical analysis, and dynamics},
  author={Mihelic, SA and Engelmann, SA and Sadr, MS and Jafari, CZ and Zhou, A and Williamson, MR and Dunn, AK},
  year={2023}
}

V2.0.2 (Iva Patch 2)

This release redefines a hard-coded parameter in the edge extraction step, which was changed in the V2.0.1 (Iva patch) version, resulting in less sensitive bifurcation detection. The parameter is reset to the value in the V2.0.0 (Iva) version.

• SAM 5/11/22

V2.0.1 (Iva Patch)

This release is a patch on the V2 (Iva) version. This patch fixes the following the issue: manually added vertices were unable to form edges automatically.

Additionally, the histogram (both area and network) analyses have been improved, changing the PDFs and CDFs displayed from discrete (binned) to continuous (smoothed) functions.

SAM 5/2/22

Note: the working-dir.zip attachment has just the source code (not the tutorial or other readme's) in a single folder for ease of use.

V2 (Iva)

SAM 3/1/22

This v2 version (Iva) builds upon the initial (debut) release (publication) in several ways:

Edge extraction is improved from random walks in parallel to an image operation akin to a sparse and directed watershed method. The edges (and thus strands) extracted from this new method are more realistic, better behaved, and have more accurate statistical properties. Hard directional- and soft size- and length-constraints applied.

Edge energy metrics have been normalized, so these objects are easier to threshold globally.

Vertex energies have been log-transformed for easier histogram visualization.

Strand and area histograms have been improved and expanded, and are free of the previous bug which caused a large population of strands of shorter lengths.

Major improvements to the edge (and vertex) curator(s). Vertex visualization and addition, orthogonal projections for viewing,

The energy filtering step has been improved to have more accurate sizing (scale coordinate projection changed from a center of energy projection to a min energy projection.

Many SpecialOutput name/value pair options added: .vmv, .casx, flow-fields,

Improvements to existing SpecialOutput options

debut

First public release of the vectorization software created by Samuel Alexander Mihelic (SAM) for the Functional Optical Imaging Lab (FOIL).