Engineered heart tissues (EHTs) provide a promising platform for modeling cardiac physiology, but their dense and heterogeneous fiber organization makes quantitative analysis highly challenging. This thesis presents an automated pipeline for fiber segmentation and structural analysis of confocal EHT images. The framework integrates frequency based preprocessing using FFT bandpass filtering, state of the art deep learning segmentation models (U-Net, Attention U-Net, and U-Net++), and post-processing refinement through a secondary U-Net. Evaluation was conducted on a synthetic labeled dataset and on real EHT slices with sparse annotations. The results highlight clear trade-offs between model architectures. U-Net produced the most complete and connected fibers but introduced substantial hallucinations. Attention U-Net generated clean outputs but with fragmented fibers, and U-Net++ achieved a balance by capturing directionality and coherence with reduced continuity. Refinement networks were effective at reducing thickness and noise in some cases, but they often removed true fibers and fragmented long structures, providing limited overall benefit. Fiber level metrics and human inspection confirmed these findings, showing that orientation is captured reliably across models, while continuity and connectivity remain major challenges. Overall, the pipeline demonstrates the feasibility of automated structural analysis of EHTs and establishes a foundation for future work with improved datasets, advanced refinement strategies, and broader use of pretrained or structurally informed models. ... Read more

The current standard for organ-on-chip substrate materials is polydimethylsiloxane (PDMS). PDMS has many beneficial properties such as biocompatibility, transparency, elasticity, and easy prototyping. The main disadvantages of PDMS are its hydrophobicity (reducing cell attachment and cell proliferation), quick hydrophobic recovery (within a few hours) after surface modification, and unselective absorption of small molecules, altering drug concentration during testing or causing cross-contamination between channels. To overcome these shortcomings, an alternative material lacking the disadvantages and retaining the advantages of PDMS is needed in the field. Ostemer 324, Ostemer 220 and a variation of PDMS (PDMS+) were characterized to determine whether they would be a suitable alternative to PDMS as substrate material. The materials were compared to PDMS and characterized for spin-coating and curing on silicon wafers, moulding, etching, surface wettability before and after surface modification (plasma treatment), stiffness, optical transparency, biocompatibility and absorption of small molecules. The results of this work show that Ostemer 324 appears to be a promising alternative, with similar characteristics to PDMS. The main advantage is its hydrophilic surface, which becomes even more hydrophilic after plasma treatment, and slow hydrophobic recovery rate. However, its curing time is longer, the material is stiffer and not easy to mould. Ostemer 220 shows very poor adhesion on Teflon coated silicon wafers, is hard to mould, and shows inconsistent results during biocompatibility testing. PDMS+ is very similar to PDMS, and improves upon the latter in terms of surface wettability after surface modification, hydrophobic recovery and small molecule absorption. ... Read more

Engineered Heart Tissues (EHTs) are a valuable approach enabled by Organ-on-Chip (OoC) technology to model human cardiac tissue. These small microfluidic devices allow the culture and development of living cardiac cells in 3D structures, to reproduce tissue dynamics and functionality in-vitro, thus fostering the development of new and more precise models for human diseases and organs’ physiological response.
One of the most important gaps in this recent technology is the lack of integration of electronic devices in the platforms, such as electrodes for tissue stimulation or sensors for real-time monitoring of the tissue.

To cover this gap, a polymer-based platform with microwell and micropillars for culturing EHTs and measuring their contractile properties was developed in ECTM group at TU Delft. The contraction force exerted by the beating cardiac tissue, self-assembled around the micropillars, is quantified by measuring the displacement of the micropillars with spiral capacitive sensors embedded in the substrate. The force generated by the tissue corresponds to a capacitance change which is simulated to be in the aF range, requiring a high-precision, sensitive, and portable read-out circuitry.

The investigation and development of this readout electronics is the final goal of this Master Thesis. A literature survey about possible capacitive readout techniques was conducted to identify suitable architectures for measuring such small dynamic changes in capacitance. Two solutions available on the market (Smartec UTI and Analog Devices AD7746) implementing two of these architectures were chosen, tested, and characterised. Benchmark measurements with accurate laboratory instrumentation were performed, and noise figures of the two solutions were evaluated.
To allow the readout, EHT platforms with embedded sensors need to be transferred and assembled on a custom Printed Circuit Board (PCB): the viability of this challenging assembly process was evaluated. The multiple constraints deriving from such a complex project determined the development of a non-standard assembly process, which proved to be delicate and gave origin to multiple failure modes. Those were documented and analysed, to identify alternative or improved assembly procedures which need to be developed to fabricate reliable samples, since these weaknesses were identified as the most critical aspect at this point of the project.

The results obtained showed how the two solutions for the readout provided results in good agreement with more precise non-portable laboratory instrumentation, and promising noise figures. The platforms with embedded sensors were successfully transferred to the developed PCBs, and measurements showed good agreement with the simulated static behaviour of the sensors, thus providing a valuable proof-of-concept for the whole project.
The dynamic behaviour of the sensors was preliminarily investigated and characterized using nanoindentation tests, indicating the possibility to measure a linear relationship between the force applied and the difference in the sensed capacitance. Despite this good result, further tests need to be performed to verify it and to address some criticalities that were identified.
Cardiac tissue was cultured on platforms with integrated sensors and the biocompatibility of the entire system was proved. The behaviour of the sensors during biological measurement with cardiac cells is left to future investigation. ... Read more