Skip to content
Computational Biophysics and Imaging Group

Infrastructure and Software

Infrastructure

Our facilities include 3D microstructure imaging instrumentation, bioimpedance and cellular electrophysiology. Please see a virtual tour of our imaging labs.

  • CBIG is running a state of the art 0.6 µm resolution µCT system capable of analyzing the microstructures of various materials and constructs including biomaterials, ceramics, electronic manufactured constructs, biofluidic systems as well as tissues and cells.
  • We have an in-house build optical projection tomography imaging system for imaging hydrogel cultures and cells. This is been expanded to include Single Plane Illumination Microscope (SPIM) as well.
  • We are also part of the Tampere imaging facility
  • BioMediTech and CBIG have a state of the art bioelectric/biomimetic technology laboratory featuring six sets of commercial microelectrode array bioelectric instrumentations including a new 4000 channel CMOS HD multielectrode array, 800 electrode multiwall MEA systems, 3D commercial MEA systems with 60 channel stage, two separate stages with full patch clamp and fluorescence imaging systems as well as various electric, light, and mechanical stimulus systems for cells.
  • We have state of the art impedance spectroscopy instrumentations (Solatron and Zurich instrument impedance analyzers) for assessing electrical impedance of tissues, cell samples, electrodes or other materials.

Software tools

We have developed software that are available at:

  • Automatic objective neuronal spike detection for electrophysiological measurements (Code, Paper)
  • CardioMDA: Cardiomyocyte MEA Data Analysis (CardioMDA) software is a simple and semi-automated tool to analyze and evaluate drug response in cardiomyocyte cell population from field potential recordings. This offline analysis tool is designed to improve accuracy and reliability of drug screening. (Code, Paper)
  • CorSE: Spectral entropy based neuronal network synchronization analysis for extracellular electrophysiological data (Code, Paper, Thesis)
  • ε-recurrence network analysis toolbox: The codes in the toolbox can be used to perform nonlinear time series analysis on single (or multi) channel data (Code, Paper, Thesis, Codes for nonlinear time series analysis)
  • Joint analysis of extracellular spike waveforms and neuronal network bursts (Code, Paper, Thesis)
  • SimpleCTC: Software that computes the contour tree connectivity (CTC) of 2D/3D images roviding e.g. information on material porosity (Code, Paper, Thesis)
  • Network-Wide Adaptive Burst Detection Depicts Neuronal Activity with Improved Accuracy: a modified version of the cumulative moving average (CMA) algorithm (Code, Paper)
  • Computational models of excitation-contraction coupling in human induced pluripotent stem cell-derived cardiomyocyte: Matlab codes for the 2021 version (Publication) and 2022 version (Publication) are available upon request from mohamadamin.forouzandehmehr@tuni.fi.

Models

  • Tight junctions structural dynamics model for molecular permeability and transepithelial resistance (model available as Supporting Information with the Paper)
  • In silico models of human induced pluripotent stem cell-derived cardiomyocyte action potentials and calcium transients. The Matlab code of both the 2013 version (Paper) and the 2018 version (Paper) are available upon request
  • INEXA: Code can be downloaded from here