Data from: Atypical collective oscillatory activity in cardiac tissue uncovered by optogenetics
Data files
Dec 19, 2025 version files 20.50 GB
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experimental_data_resonance-001.tar.gz
20.50 GB
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README.md
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Abstract
Many biological processes emerge as frequency-dependent responses to trains of external stimuli. Heart rhythm disturbances, i.e., cardiac arrhythmias, are important examples as they are often triggered by specific patterns of preceding stimuli. In this study, we investigated how ectopic arrhythmias can be induced by external stimuli in cardiac tissue containing a localised area of depolarisation. Using optogenetic in vitro experiments, we systematically explored the dynamics of these arrhythmias, which are characterized by local oscillatory activity. Our findings reveal a bi-stable system, in which transitions between oscillatory ectopic activity and a quiescent state can be precisely controlled, i.e., by adjusting the number and frequency of propagating waves through the depolarized area, oscillations could be turned on or off. These frequency-dependent responses arise from collective mechanisms involving stable, non-self-oscillatory cells, contrasting with the typical role of self-oscillations in individual units within biophysical systems.
Dataset DOI: 10.5061/dryad.dz08kpsbh
Description of the data and file structure
Neonatal rat ventricular myocyte (NRVM) monolayers were optically mapped using the voltage-sensitive dye di-4-ANBDQBS (52.5 μM final concentration; ITK diagnostics, Uithoorn, the Netherlands). The mapping setup was based on a 100 × 100 pixel CMOS Ultima-L camera (Scimedia, Costa Mesa, CA). The field of view was 16 × 16 mm, resulting in a spatial resolution of 160 μm/pixel. For targeted illumination of monolayers, the setup was optically conjugated to a digitally controlled micro-mirror device (DMD), the Polygon 400 (Mightex Systems, Toronto, ON), with a high-power blue (470 nm) LED (BLS-LCS-0470-50-22-H, Mightex Systems). Before starting the actual experiments, all monolayers were mapped during 1-Hz electrical point stimulation to check baseline conditions. Electrical stimulation was performed by applying 10-ms-long rectangular electrical pulses with an amplitude of 8 V to a bipolar platinum electrode with a spacing of 1.5 mm between anode and cathode. Only cultures with an action potential duration (APD) at 80% repolarization (APD80) below 350 ms and a conduction velocity (CV) above 18 cm/s were used for further experiments. Stimuli were applied in trains that varied in number and period. Whenever the outcome was reproducible three consecutive times in a single monolayer, it was counted as successful and included as one measurement in the total dataset. The constant light intensity was varied in the range of (0.03125-0.25 mW /mm2) to search the critical value for the bi-stable regime. For experiments in which the light intensity was varied the rectangular-shaped area of illumination was in the range of 4 × 4 to 6 × 6 mm. The highest achievable irradiation intensity (0.3125 mW /mm2) was used to perform size modulation experiments. The resulting electrical activity was recorded for 6-24 s at exposure times of 6 ms per frame.
Files and variables
File: experimental_data_resonance-001.tar.gz
Description: Contains the folders "normal resonance" (Figure 2, Figure 4-figure supplement 1), "2 vs 4" (Figure 3) and "Small_pattern-resonance" (Figure 4-figure supplement 2), each with subfolders denoting one monolayer. Within each subfolder, different recordings can be found using the .rsh and .rsd file format. They always start with a control measurement named 1Hz. Afterwards, the file names exactly describe what kind of protocol is being used, either denoting an external wave train pacing cycle length, the number of external pulses, or both (becomes clear when putting the figures next to the filenames). If a filename mentions resonance, bifurcation, or initiation, our discovered phenomenon of atypical collective oscillatory activity can be seen in those data. The regimes where this does (not) occur are described in detail in our manuscript.
Code/software
The .rsh and .rsd files can be converted to numpy arrays using sappho, an open source software package from [1]. You can access/download it directly using the following link: https://gitlab.com/heartkor/sappho. A README, installation instructions and usage examples are provided in the accompanying documentation, directly accessible via: https://heartkor.gitlab.io/sappho/. When you install the graphical user interface, you can directly select the files from your system folder and open/view them.
[1] Kabus, D., De Coster, T., de Vries, A. A., Pijnappels, D. A., & Dierckx, H. (2024). Fast creation of data-driven low-order predictive cardiac tissue excitation models from recorded activation patterns. Computers in Biology and Medicine, 169, 107949.
Raw optical mapping data were obtained using a mapping setup containing a 100 × 100 pixel CMOS Ultima-L camera (Scimedia, Costa Mesa, CA). The field of view was 16 × 16 mm, resulting in a spatial resolution of 160 μm/pixel. For targeted illumination of monolayers, the setup was optically conjugated to a digitally controlled micro-mirror device (DMD), the Polygon 400 (Mightex Systems, Toronto, ON), with a high-power blue (470 nm) LED (BLS-LCS-0470-50-22-H, Mightex Systems). Electrical stimulation was performed by applying 10-ms-long rectangular electrical pulses with an amplitude of 8 V to a bipolar platinum electrode with a spacing of 1.5 mm between anode and cathode. Data was captured in .rsh and .rsd format.