In2Sight mantains two repositories on Github regarding the software to perform the digital pathology analysis on the H&E stained histological sections and the software fopr the agent based simulation platform on MATLAB (2D).

• Digital pathology. This is the repository of the IN2SIGHT (GA.964481) project WP4 (“In-vivo validation of IN2SIGHT”).
  It contains at August 2025, two major jupiter codes. Code_HE: Analysis_Hematoxylin-Eosin_Clustering.ipynb AND Code_NLM: Analysis_NONLINEAR_Clustering.ipynb
  Both files assume that the input data have been obtained by applying QuPath (ver: QuPath-0.5.1) to the image to be classified. We first use Code_HE to build the Binary Features Vectors (BFV) for as many cell types as possible gthat can be found in the tissue. Then, we use the QuPath segmentation tool on a non-linear excitation image and apply Code_NLM to the QuPAth output giving in input also the set of BFV for each of the cell types.
  
  
• Fibro-Macrophage model. This repository contains the matlab code to run simulations of the interaction of macrophages with a immunogrenic stimulus – either a chemical stimulus or a biomaterial – within the agent based approach. It is a 32D model used to develop the equations and parameters for the engine of the single cells. It is the basis for the 3D model based on Cell Studio.

All codes in this repository are licensed under EUPL. https://interoperable-europe.ec.europa.eu/collection/eupl/documentation-repository