Data from: Organic electro-scattering antenna: Wireless and multisite probing of electrical potentials with high spatial resolution
Data files
Dec 17, 2024 version files 29.91 GB
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Data_OCEAN.zip
29.91 GB
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README.md
20.29 KB
Abstract
Monitoring electrical potentials with high recording site density and micrometer spatial resolution in liquid is critical in biosensing. Organic electronic materials have driven remarkable advances in the field due to their unique material properties, yet limitations in spatial resolution and recording density remain.
Here, we introduce organic electro-scattering antennas (OCEANs) for wireless, light-based probing of electrical signals with micrometer spatial resolution, potentially from thousands of sites. The technology relies on the unique dependence of poly(3,4-ethylenedioxythiophene):polystyrene sulfonate light scattering properties to its doping level. Electro-optic characteristics of individual antennas varying in diameters and operating voltages were systematically characterized in saline solution. Signal-to-noise ratios up to 48 were achieved in response to 100 mV stimuli, with 2.5 mV detection limits and 5 μm spatial resolution. OCEANs demonstrated milliseconds time constants and exceptional long-term stability, enabling continuous recordings over 10 hours.
By offering exceptional 5μm spatial resolution and 4.106 cm-2 recording density, OCEANs unlock new readout capabilities, potentially accelerating fundamental and clinical research.
README: Data from: Organic electro-scattering antenna: Wireless and multisite probing of electrical potentials with high spatial resolution
This dataset contains all files required to reproduce the results in the publication "Organic electro-scattering antenna: wireless and multisite probing of electrical potentials with high spatial resolution." It is organized into three sections:
- Experiments: Raw and processed data, analysis code, and output figures related to the experimental characterization of OCEAN.
- Modeling: Finite element model files, analysis code, and output figures related to the theoretical modeling of OCEAN.
- Rendering: Blender model of the antenna and rendered figures used for visualization.
The CSV file titled files_to_figures.csv (Data/files_to_figures.csv) provides a tabular summary of the files required to generate each figure, indicating their locations within the dataset and offering a brief description of their purpose.
Description of the data and file structure
Data/Experiments/Optical microscope
Includes all raw and processed optical microscope images, along with the resulting output figures and variables derived from their analysis.
Data/Experiments/Optical_microscope/Image_sequences
Includes all raw and processed optical microscope image sequences, along with the resulting output figures and variables derived from their analysis.
Data/Experiments/Optical_microscope/Image_sequences/Data_raw
Contains all raw dark-field optical microscope image sequences, categorized as follows:
- CA: Image sequences captured during ChronoAmperometry experiments.
- CV: Image sequences captured during Cyclic Voltammetry experiments.
- LT: Image sequences captured during Long-Term experiments.
- TC: Image sequences captured during Time Constant experiments.
Data/Experiments/Optical_microscope/Image_sequences/Data_processed
Contains all dark-field optical microscope image sequences processed using the Vibration Compensation algorithm, categorized as follows:
- CA_VC: Processed image sequences from ChronoAmperometry experiments.
- CV_VC: Processed image sequences from Cyclic Voltammetry experiments.
- LT_VC: Processed image sequences from Long-Term experiments.
- TC_VC: Processed image sequences from Time Constant experiments.
Data/Experiments/Optical_microscope/Image_sequences/Output
Contains all figures and output variables derived from dark-field optical microscope images, organized as follows:
- CA: Figures and variables from ChronoAmperometry experiments.
- CA_tED_30s_VC_export: Figures and variables from Chronoamperometry experiments with small OCEANs (electrodeposition time = 30 s).
- CA_tED_30s_VC_CA_VB_1 to 7: Figures displaying the optical traces of individual OCEANs in response to voltage stimuli, tested under operating bias voltages ranging from 0V (1) to -0.6V (7).
- CA_tED_30s_VC_Sensitivity: Figures illustrating the variation in optical signal in response to voltage for the different operating biases tested.
- CA_tED_30s_VC_variables.mat: MATLAB variables capturing the optical signal response to voltage for each antenna tested experimentally.
- CA_tED_45s_VC_export: Figures and variables from Chronoamperometry experiments with intermediate OCEANs (electrodeposition time = 45 s).
- CA_tED_45s_VC_CA_VB_1 to 7: Figures displaying the optical traces of individual OCEANs in response to voltage stimuli, tested under operating bias voltages ranging from 0V (1) to -0.6V (7).
- CA_tED_45s_VC_Sensitivity: Figures illustrating the variation in optical signal in response to voltage for the different operating biases tested.
- CA_tED_45s_VC_variables.mat: MATLAB variables capturing the optical signal response to voltage for each antenna tested experimentally.
- CA_tED_60s_VC_export: Figures and variables from Chronoamperometry experiments with large OCEANs (electrodeposition time = 60 s).
- CA_tED_60s_VC_CA_VB_1 to 7: Figures displaying the optical traces of individual OCEANs in response to voltage stimuli, tested under operating bias voltages ranging from 0V (1) to -0.6V (7).
- CA_tED_60s_VC_Sensitivity: Figures illustrating the variation in optical signal in response to voltage for the different operating biases tested.
- CA_tED_60s_VC_variables.mat: MATLAB variables capturing the optical signal response to voltage for each antenna tested experimentally.
- CA_comparison: Figures summarizing the impact of OCEAN geometry and operating biases on key performance metrics, including sensitivity, noise, signal-to-noise ratio (SNR), and limit of detection (LOD).
- HIST_: Histograms showing the distribution of performance metrics across antennas
- _comparison: Figures showing the impact of OCEAN geometry and operating biases on performance metrics
- CV: Figures and variables from Cyclic Voltammetry experiments.
- CV_tED_30s_VC_export: Figures and variables from Cyclic Voltammetry experiments with small OCEANs (electrodeposition time = 30 s).
- CV_tED_30s_VC_CV: Figures illustrating the variation of OCEAN optical signal and current in response to voltage sweep between -0.8V to 0.7V.
- CV_tED_30s_VC_variables.mat: MATLAB variables capturing the variation of optical signal in response to voltage sweep for each antenna tested experimentally.
- CV_tED_45s_VC_export: Figures and variables from Cyclic Voltammetry experiments with intermediate OCEANs (electrodeposition time = 45 s).
- CV_tED_45s_VC_CV: Figures illustrating the variation of OCEAN optical signal and current in response to voltage sweep between -0.8V to 0.7V.
- CV_tED_45s_VC_variables.mat: MATLAB variables capturing the variation of optical signal in response to voltage sweep for each antenna tested experimentally.
- CV_tED_60s_VC_export: Figures and variables from Cyclic Voltammetry experiments with large OCEANs (electrodeposition time = 60 s).
- CV_tED_60s_VC_CV: Figures illustrating the variation of OCEAN optical signal and current in response to voltage sweep between -0.8V to 0.7V.
- CV_tED_60s_VC_variables.mat: MATLAB variables capturing the variation of optical signal in response to voltage sweep for each antenna tested experimentally.
- CV_comparison: Figures summarizing the impact of OCEAN geometry on cyclic voltammetry results.
- LT: Figures and variables from Long Term characterization experiments.
- LT_Xh_VC_: Figures and variables from Long Term experiments at time X.
- Zscore: Figure showing optical signal variation in response to -100 mV voltage pulse at time X.
- variables.mat: MATLAB variables capturing the variation of optical signal in response to -100 mV voltage pulses for each antenna tested experimentally at time X.
- TC: Figures and variables from Time Constant experiments.
- TC_tED_30s_VC_export: Figures and variables from Time Constant experiments with small OCEANs (electrodeposition time = 30 s).
- TC_tED_30s_VC_Time_constant: Figures illustrating the variation of OCEAN optical signal in response to -100 mV voltage pulses with fast acquisition frame rate.
- TC_tED_30s_VC_variables_TC.mat: MATLAB variables capturing the variation of optical signal in response to -100 mV voltage pulses with fast acquisition frame rate for each antenna tested experimentally.
- TC_tED_45s_VC_export: Figures and variables from Time Constant experiments with intermediate OCEANs (electrodeposition time = 45 s).
- TC_tED_45s_VC_Time_constant: Figures illustrating the variation of OCEAN optical signal in response to -100 mV voltage pulses with fast acquisition frame rate.
- TC_tED_45s_VC_variables_TC.mat: MATLAB variables capturing the variation of optical signal in response to -100 mV voltage pulses with fast acquisition frame rate for each antenna tested experimentally.
- TC_tED_60s_VC_export: Figures and variables from Time Constant experiments with large OCEANs (electrodeposition time = 60 s).
- TC_tED_60s_VC_Time_constant: Figures illustrating the variation of OCEAN optical signal in response to -100 mV voltage pulses with fast acquisition frame rate.
- TC_tED_60s_VC_variables_TC.mat: MATLAB variables capturing the variation of optical signal in response to -100 mV voltage pulses with fast acquisition frame rate for each antenna tested experimentally.
- TC_comparison: Figures summarizing the impact of OCEAN geometry and operating biases on time constant.
Data/Experiments/Optical_microscope/Images
Includes all raw optical microscope images, along with the resulting output figures and variables derived from their analysis.
Data/Experiments/Optical_microscope/Images/Data_raw
Contains all raw optical microscope images, categorized as follows:
- CV: Dark field microscopy images extracted from CV at -0.8V for small (Vmin_30s), intermediate (Vmin_45s), and large (Vmin_60s) antennas.
- tED_: Brightfield images showing OCEAN arrays before (No_ED.tif) and after (tED_30s.tif, tED_45s.tif, tED_60s.tif) electrodepostion.
Data/Experiments/Optical_microscope/Images/Output
Contains all figures and output variables derived from brightfield optical microscope images, organized as follows:
- tED_XXs_: Figures summarizing the output of the image processing pipeline developed to estimate the dimensions of OCEANs following different electrodeposition times (XX s).
- tED_XXs_diameters.mat: MATLAB variables summarizing the measured diameters of OCEANs following different electrodeposition times (XX s).
Data/Experiments/Potentiostat
Includes all raw data acquired with the potentiostat, along with the resulting output figures and variables derived from their analysis.
Data/Experiments/Potentiostat/Data_raw
Contains all raw data acquired with the potentiostat, organized as follows:
- CA: Data captured during ChronoAmperometry experiments for small, intermediate, and large antennas.
- CV: Data captured during Cyclic Voltammetry experiments for small, intermediate, and large antennas.
- EIS: Data captured during Electrochemical Impedance Spectroscopy experiments for small, intermediate, and large antennas at different operating biases:
- EIS_tED_XXs: EIS data for antennas electrodeposited during XX s.
- P_30s_EIS_E_XV: EIS data for small antennas at X V operating votlage (m = minus).
- TC: Data captured during Time Constant experiments for small, intermediate, and large antennas.
Data/Experiments/Potentiostat/Output/EIS
Contains all figures and output variables derived from electrochemical impedance spectroscopy data, organized as follows:
- EIS_tED_XXs_EIS: Electrochemical impedance spectroscopy plots for small (tED = 30 s), intermediate (tED = 45 s), and large (tED = 60 s) OCEAN arrays under different voltage biases ranging from -0.6V to 0V.
- EIS_comparison: Figures showing the impact of OCEAN geometry and operating voltage on the electrical equivalent circuit component values.
- TC_vs_bias: Figures illustrating the predicted impact of OCEAN geometry and operating voltage on time constant.
Data/Experiments/Spectrometer
Includes all raw data acquired with the optical spectrometer, along with the resulting output figures and variables derived from their analysis.
Data/Experiments/Spectrometer/Data_raw
Contains relative irradiance raw files acquired with the spectrometer from OCEAN arrays under different votlage biases, organised as follows:
- XX_RelativeIrradiance_: Relative irradiance from OCEAN arrays at XX V operating bias from 0V to -0.7V (M = minus).
Data/Experiments/Spectrometer/Output
Includes a figure showing OCEAN array relative irradiance spectrums with respect to operating voltage.
Data/Experiments/Code
Includes all the MATLAB codes used to analyse the experimental data presented in this section, organized as follows:
- CA_ANALYSIS.m: MATLAB code for analyzing data from Chronoamperometry experiments and generating output files located in Data/Experiments/Optical_microscope/Image_sequences/Output/CA
- CV_ANALYSIS.m: MATLAB code for analyzing data from Cyclic Voltammetry experiments and generating output files located in Data/Experiments/Optical_microscope/Image_sequences/Output/CV
- LT_ANALYSIS.m: MATLAB code for analyzing data from Long Term experiments and generating output files located in Data/Experiments/Optical_microscope/Image_sequences/Output/LT
- LT_COMPARISON.m: MATLAB code for comparing OCEAN long-term characteristics across electrodeposition conditions and generating output files located in Data/Experiments/Optical_microscope/Image_sequences/Output/LT
- TC_ANALYSIS.m: MATLAB code for analyzing data from Time Constant experiments and generating output files located in Data/Experiments/Optical_microscope/Image_sequences/Output/TC
- EIS_ANALYSIS.m: MATLAB code for analyzing data from Electrochemical Impedance Spectroscopy experiments and generating output files located in Data/Experiments/Potentiostat/Output/EIS
- DIA_ANALYSIS.m: MATLAB code for analyzing OCEAN diameters from brightfield images and generating output files located in Data/Experiments/Optical_microscope/Images/Output
- DIA_COMPARISON.m: MATLAB code for comparing OCEAN diameters across electrodeposition conditions and generating output files located in Data/Experiments/Optical_microscope/Images/Output
- EO_EIS_characteristics_comparison.m: MATLAB code for comparing OCEAN electro-optic and electrochemical characteristics across electrodeposition conditions and generating output files located in Data/Experiments/Optical_microscope/Image_sequences/Output/
- Spectrum_analysis.m: MATLAB code for analyzing OCEAN relative irradiance spectrums and generating output files located in Data/Experiments/Spectrometer/Output
- TC_vs Bias.m: MATLAB code for predicting the impact of votlage bias and OCEAN geometry on Time Constant from electrochemical impedance spectroscopy data and generating output files located in Data/Experiments/Potentiostat/EIS/Output
- Vibration_compensation_V2.m: MATLAB code for applying vibration compensation to raw image sequences and generating output files located in Data/Experiments/Optical_microscope/Image_sequences/Data_processed
Additional .m files are dependencies required to run the MATLAB scripts.
Data/Modeling/Permittivity_PEDOTPSS
Contains all data and code required to compute PEDOT:PSS dielectric functions for different bias voltages in phosphate buffered saline, along with the resulting output figures and variables from the analysis, organized as follows:
- Code: Contains all scripts required to compute the dielectric functions of PEDOT:PSS under various voltage biases in phosphate-buffered saline solution.
- PEDOTPSS_permittivity.m: MATLAB code for calculating the dielectric functions of PEDOT:PSS across different voltage biases. Additional .m files are dependencies required to run the PEDOTPSS_permittivity.m script.
- Data: Includes optical data from Cyclic Voltammetry experiment required by PEDOTPSS_permittivity.m
- Output: Contains all output files and figures related to the voltage dependence of PEDOT:PSS dielectric functions, organized as follows:
- dielectric_function_parameters: A CSV file with computed parameters of PEDOT:PSS dielectric functions, generated by PEDOTPSS_permittivity.m.
- PEDOTPSS_dielectric_functions: Text files detailing the dielectric functions of PEDOT:PSS under various bias voltages.
- Figures: Visual representations of PEDOT:PSS dielectric functions across different voltage biases and doping levels, including a sigmoid relationship between doping level and voltage, created using PEDOTPSS_permittivity.m.
Data/Modeling/Scattering_cross_section
Contains all data, model files, and code necessary to compute OCEAN scattering cross-sections for various bias voltages and dimensions, along with the resulting output figures. The content is organized as follows:
- Code: Includes OCEAN_analysis.m, a MATLAB script for processing scattering cross-section data from finite element simulations performed in CST Studio.
- Model_file: Contains OCEAN.cst, the CST Studio file used for finite element simulations of OCEAN scattering cross-sections.
- Data: Provides all computed scattering cross-section data for OCEANs with diameters of 750 nm (D750) and 1500 nm (D1500) at different operating voltages.
- Output: Includes figures illustrating the effect of OCEAN geometry and operating biases on scattering cross-sections, derived from finite element simulations.
Data/Modeling/Effect_of_cell
Contains all data, model files, and code required to compute OCEAN scattering cross-sections with a cell on top, as well as the resulting output figures. The content is organized as follows:
- Code: Includes analysis.m, a MATLAB script for analyzing scattering cross-section data from finite element simulations performed in CST Studio.
- Model: Contains OCEAN.cst, the CST Studio file used for finite element simulations of OCEAN scattering cross-sections with a cell positioned on top.
- Data: Provides simulated scattering cross-section data for OCEANs with and without cells, illuminated under regular or total internal reflection dark-field configurations at various voltage conditions.
- Output: Includes figures showing the effect of a cell on OCEAN scattering cross-sections across different optical configurations, derived from finite element simulations.
Data/Modeling/AP_recording_OCEANs
Contains the necessary code required to compute the voltage drop across OCEAN during intracellular recording of cardiomyocyte action potentials, performed under voltage- and current-clamp configurations, along with the resulting output figures.
Data/Modeling/AP_recording_OCEANs/Current_clamp_OCEANs
Contains the necessary code required to compute the voltage drop across OCEAN during intracellular recording of cardiomyocyte action potentials, performed under current-clamp configuration, along with the resulting output figures. The content is organized as follows:
- Code: Contains the scripts necessary to implement the Luo-Rudy model adapted for OCEANs:
- CC_OCEAN_LR91.m: Computes the cardiomyocyte action potential waveform and its attenuation across OCEAN in current-clamp (CC) configuration.
- dydt_CC_OCEAN_LR91.m: Function for solving the system of differential equations in the CC configuration.
Output: Provides figures illustrating the expected voltage across OCEANs during intracellular recording of cardiomyocyte action potentials in the CC configuration.
Data/Modeling/AP_recording_OCEANs/Voltage_clamp_OCEANs
Contains the necessary code required to compute the voltage drop across OCEAN during intracellular recording of cardiomyocyte action potentials, performed under voltage-clamp configuration, along with the resulting output figures. The content is organized as follows:
- Code: Contains the scripts necessary to implement the Luo-Rudy model adapted for OCEANs:
- VC_OCEAN_LR91_V5.m: Computes the cardiomyocyte action potential waveform and its attenuation across OCEAN in voltage-clamp (VC) configuration.
- dydt_VC_OCEAN_LR91_V5.m: Function for solving the system of differential equations in the VC configuration.
Output: Provides figures illustrating the expected voltage across OCEANs during intracellular recording of cardiomyocyte action potentials in the VC configuration.
Data/Rendering
Contains the Blender file used for OCEAN rendering. The rendered figures are available in the Output folder.
Code/Software
The analyses were performed using MATLAB 2023. All codes and functions have been described in detail in the "Description of the Data and File Structure" section, and all dependencies, including MATLAB code functions, are provided within the dataset to ensure reproducibility.