A repository for the freely available software - IVEN (Internal Versus External Neighbourhood quantification). Original journla article can be found at https://doi.org/10.1371/journal.pbio.3001345 . IVEN is a platform that is able to help anlayse biological datasets and interrogate the neighbourhood characteristics of systems. Cells are classified as inside or outside using the convex hull algorithm and subsequently the number of neighbours of cells are calculated using a 'corrected' Delaunay Triangulation.
Python 3 Version:
Set-up using virtual environment generated from included requirements.txt file. User interface available to facilitate manual cell classification, cavity-adjacent cell calculation and threshold selection. Results output to .csv files.
MATLAB Version:
(discontinued)
Available in the v1.0.0 release.
Tutorials Available:
-IVEN Neighbour Distance Threshold Advice
-IVEN Use in Python
-VIDEO: Python IVEN
-VIDEO: Python display figure after analysis
Help in implementing the code:
Contact jessforsyth95@gmail.com with screenshots and details description of any issues with implementation. Please refer to the videos and video tutorials first for quick help on how to use IVEN.