git-annex in @med068pc183

README.md

@@ -7,7 +7,7 @@ Neuro Group, Faculty of Medicine and Health Technology, Tampere University
 
 ## Summary
 
-We provide a dataset of microelectrode array recordings (MEA) from human pluripotent stem cell (hPSC)-derived and rat embryonic cortical neurons during in vitro maturation and pharmacological treatment at their mature stage ([Kapucu et al., submitted](http://doi.org/to-be-inserted-after-publication)). Together with the recorded raw MEA data, we share the analysis code that produces the key scientific findings published previously with this dataset ([Hyvärinen et al., 2019](https://doi.org/10.1038/s41598-019-53647-8)), including PCA analysis to reveal the distinction between rat and human cell activity features. The data enables evaluation and comparison of hPSC-derived and rat cortical cultures in terms of functional development and response to pharmacological treatment. The 12500 Hz sampled data is recorded with Axion 12-well plates (for developmental tracking) and 48-well plates (for pharmacological experiments). Raw data constitute time series of extracellularly recorded voltage values in Volts. The duration of the recordings varies from 10 to 30 minutes depending on the experimental set-up. Each raw MEA data file contains organised meta-data. This dataset is valuable for experimental and computational neuroscientists and any signal analyst with interest for neuronal signalling. The accurate detailed description of data is delivered in the corresponding publication ([Kapucu et al., submitted](http://doi.org/to-be-inserted-after-publication)). Please, refer to the publication, as this README.md file deliver only a brief introduction of the data and basic procedures of reading it.
+We provide a dataset of microelectrode array recordings (MEA) from human pluripotent stem cell (hPSC)-derived and rat embryonic cortical neurons during in vitro maturation and pharmacological treatment at their mature stage ([Kapucu et al., 2022](https://doi.org/10.1038/s41597-022-01242-4)). Together with the recorded raw MEA data, we share the analysis code that produces the key scientific findings published previously with this dataset ([Hyvärinen et al., 2019](https://doi.org/10.1038/s41598-019-53647-8)), including PCA analysis to reveal the distinction between rat and human cell activity features. The data enables evaluation and comparison of hPSC-derived and rat cortical cultures in terms of functional development and response to pharmacological treatment. The 12500 Hz sampled data is recorded with Axion 12-well plates (for developmental tracking) and 48-well plates (for pharmacological experiments). Raw data constitute time series of extracellularly recorded voltage values in Volts. The duration of the recordings varies from 10 to 30 minutes depending on the experimental set-up. Each raw MEA data file contains organised meta-data. This dataset is valuable for experimental and computational neuroscientists and any signal analyst with interest for neuronal signalling. The accurate detailed description of data is delivered in the corresponding publication ([Kapucu et al., 2022](https://doi.org/10.1038/s41597-022-01242-4)). Please, refer to the publication, as this README.md file deliver only a brief introduction of the data and basic procedures of reading it.
 
 ## Downloading the data
 
@@ -112,7 +112,7 @@ To launch the connectivity analysis, the user needs to open the *Connectivity.m*
 
 
 ## Related Publications
-* Kapucu, F.E., Vinogradov A., Hyvärinen T., Ylä-Outinen L., Narkilahti S. Comparative microelectrode array dataset of functional development of human PSC-derived and rat neuronal networks. Submitted
+* Kapucu, F.E., Vinogradov A., Hyvärinen T., Ylä-Outinen L., Narkilahti S (2022). Comparative microelectrode array dataset of functional development of human PSC-derived and rat neuronal networks. Scientific Data volume 9, 120. https://doi.org/10.1038/s41597-022-01242-4
 * Hyvärinen, T., Hyysalo, A., Kapucu, F.E., Aarnos, L., Vinogradov, A., Eglen, J.E., Ylä-Outinen, L., Narkilahti, S. (2019). Functional characterization of human pluripotent stem cell-derived cortical networks differentiated on laminin-521 substrate: comparison to rat cortical cultures. Scientific Reports volume 9, 17125. https://doi.org/10.1038/s41598-019-53647-8
 
 ## Funding
@@ -125,7 +125,7 @@ To launch the connectivity analysis, the user needs to open the *Connectivity.m*
 
 The directory `Codes\MATLAB spike detection` contains folder `Functions from F. Lieb's SpikeDetection-Toolbox` which embeds functions imported from [SpikeDetection-Toolbox](https://github.com/flieb/SpikeDetection-Toolbox) distributed under GNU General Public License v3.0. 
 
-The directory `Codes` contains folder `meaRtools` with modified version of [meaRtools package](https://github.com/igm-team/meaRtools) distributed under GNU General Public License v3.0. Modifications imply user interface, input file reading and selection process and the addition of [LogISI algorithm](https://doi.org/10.1007/s10827-009-0175-1) for burst detection into the package. The LogISI algorithm originally received from its author Valentina Pasquale was modified for our data and the modifications are described in the publication [Kapucu et al., submitted](http://doi.org/to-be-inserted-after-publication). 
+The directory `Codes` contains folder `meaRtools` with modified version of [meaRtools package](https://github.com/igm-team/meaRtools) distributed under GNU General Public License v3.0. Modifications imply user interface, input file reading and selection process and the addition of [LogISI algorithm](https://doi.org/10.1007/s10827-009-0175-1) for burst detection into the package. The LogISI algorithm originally received from its author Valentina Pasquale was modified for our data and the modifications are described in the publication [Kapucu et al., submitted](https://doi.org/10.1038/s41597-022-01242-4). 
 
 The directory `Codes` contains folder `Connectivity Analysis` with [Spectral entropy based neuronal network synchronization analysis: CorSE](https://doi.org/10.3389/fncom.2016.00112) code distributed under the 3-Clause BSD License.