This package contains the core libraries for defining vascular trees, their bounding geometries and functional structures, and the operations to build, optimize, constrain, analyze and triangulate them. Libraries for import/export of common file formats are also provided.
This is a heavy, memory hungry package designed to solve a very limited subset of the general vasculature design problem very quickly, focussed entirely on practical tissue engineering. It does not deal with the microenvironment or functional unit design, focussing instead on tiling vessels into the mesoscale (the limit of where we actually have control over in tissue engineering). You need to do the microscale design work and run simulations or tests yourself before passing it to the methods contained here, or just guess / copy whatever real tissue looks like (it works more often than you'd expect). Similarly, it does not make adjustments for viscosity correction factors that are required at small radii, because successful tissue engineering requires the cells to remodel and actively control the vessel radii at this scale. If you need to do design work below this length scale, you'll probably want to work in subregions to generate microvasculature.
This package is currently in pre-release so APIs should not be considered stable: if you build on top of this, fix your version number!
Development is directly onto the develop branch with the exception of major rewrites, there are no guarantees that this will even build at a point in time.
Releases to NuGet will occur on a vibes-based schedule.
During Version 0.X, the minor version number will indicate breaking changes.
This is not a complete piece of software; rather, a set of libraries that may be used to build one. If you are an experimentalist and want custom networks or bespoke software for your use case without needing to write code, get in touch.
This project is licensed under the GNU Affero General Public License v3.0 (AGPL-3.0).
This project does not currently accept contributions.
- Support for variable viscosity (e.g. Fåhræus-Lindqvist effect) and some degree of variable pressure at the network outlets (e.g. two-stage networks for functional structures and surrounding capillary bed), if possible to do without a generic constrained minimization package.
- A separate package for optimization and setting radii in the most general case.
Support for higher order splitting: (0.2)Adapt splitting function and optimizer to work with n-furcations.Adapt topological actions.Fix any holes in collision/export that don't actually work with arbitrary degree splits.Merging/splitting heuristics.
- Structure:
- Multi-network sets (i.e., multiple sources over the same set of terminals) (0.3)
- Remove conditional compilation terms, or make network/branch/node generic so that data can be attached without requiring additional maps.
- Splitting:
- Amplifying downstream radii (and reducing upstream) to ensure minimum feature sizes.
- Fixed vessels (where radii fractions are always known). For imaging purposes, to be implemented using the multiple network framework and we will provide update methods to ensure pressure consistency. (0.3.x)
- Optimization:
Replace old costs with new ones.(0.2)Simplify interface to optimizer.(0.2)Integrate "soft-toplogy" and gradient descent (+ predicated movement) to ensure valid state.Remove actions queue, provide interface to rebalance+trim/regroup+split
- Reintroduce region-based transfer actions and incorporate multi-network section transfer (0.3)
- Collision:
- Intercept and ignore API for imaging/predefined roots context. (0.2.x)
- Allowing multinetwork sets to pass subsections between each other. (0.3)
- Hybrid of LSV/ACCO growth - a general purpose growth method.
- Support for multi-network growth. (0.3)
Move Vascular.Analysis and CAD interop into a separate repository, merge with rendering libraries.(removal 0.2, reintroduction 0.? - contact me if you need these bits in the meantime)- Output:
- Slice streaming as image/curve.
- Support for basic mesh options such as cutting out of a boundary.
- Input:
- Support for approximating a mesh with point sources - deriving this set of sources to be in a separate repository.
- Converting a generic graph to a network. (Loading graphs and peripheral information to be done separately).
- Housekeeping:
- Documentation and API consistency. (target: 1.0)
- Tidy up legacy bits. (target: 1.0)
Enable nullable.(0.2)Remove data contract members.(0.2)- Make the test suite available (target: 1.0)
dotnet add package Vascular.Networks
.NET 6.0
The project copies its output to a NuGet convention-based working directory in release configuration: dotnet build -c Release.
You will find the output files in /Release/lib/TFM/ for the current Target Framework Moniker.
In Debug, output files are copied to /Debug/TFM/.
Warning: at some point this will be removed
For types in the Vascular.Structure namespace, a custom build can choose to improve performance by removing fields that are not needed:
NoEffectiveLength- The most common use case for optimization is a combination of work and volume, so the branches by default keep track of their effective lengths and propagate these changes upstream, allowing instant query of the volume from the source node. Defining this disables the effective length caching.NoDepthPathLength- Path lengths and logical depths are calculated from the root downwards in a single pass and stored at each node. If defined, these fields and methods are removed. Note that some optimization predicates may require depths to be defined, although flow rate could be used as a proxy in this case.NoPressure- Pressures may be calculated downwards from the root after radii are assigned. If defined, these fields and methods are removed.
The semi-manual, mostly MSBuild based workflow has been deprecated in place of scripted release.
sudo ./setup-nuget.sh [ApiKey]
./release.sh <Version> [push]