gin commit from med068pc183

New files: 16
Deleted files: 2

Aboutarticle.txt

@@ -1,13 +0,0 @@
-Our recorded raw MEA data is stored in HDF5 format. The main features of HDF5 file format are groups and datasets. Each group can contain other groups and dataset. Each group or dataset may be assigned with attributes.In our case, each HDF5 file contain two main groups: '/Data' and '/DataInfo'. The group '/Data' includes separate group for each well labelled correspondingly. Each well group includes number of datasets: a separate dataset for each electrode of that well which contain the corresponding waveform in Volts. 
-The group '/DataInfo' contains two datasets : 'ExcludedWells' and 'InactiveChannels'; and six attributes: 'SamplingFrequencyInHz', 'DurationInSec', 'RecordingUnits', 'Volts',' DIV', 'Plate type'.
-
-To access a particular dataset the user should use specific command for HDF5 dataset reading with the corresponding HDF5 file name and the desired dataset address as its parameters.
-The same refers to the attributes of '/DataInfo' group.
-Should we have a couple of examples here?
-
-The name of each file contains the following information. The names of raw files consists of 4 blocks separated by the underscore symbol. The first block represents the origin of the cells: either "hPSC" or "Rat". The second block refers to the date of the experiment in "ddmmyy" format omitting the first zero in case of its appearance.The third block specifies the sequence MEA plate label. Please, note, that the rat and human data have same sequence labels e.g. MEA1, MEA2, etc. The fourth block designates the DIV number. 
-For pharmacological experiments the DIV label continues with the specific postfix like "Baseline", "Pharma" or "TTX" which indicates the corresponding stage of the experiment.
-
-
-
-For meaRtools, the input file set includes spike files (obtained from MATLAB for each recording day), ExpLog and the noisy electrode listing. All the mentioned files are in csv format. The Explog file contains treatment info for the corresponding analysis set (one or more DIVs) and named after the firts DIV of the experimental set. If the well is excluded from the experiment this information is recorded in the ExpLog file likewise. The Noisy electrodes "?" file contains the table of noisy electrodes for each DIV of the experimental set. These electrodes demonstrate heavily noise-contaminated waveforms and are to be excluded from the analysis to avoid distortion of the resulting statistics.

Data/PCA/hPSC_MEA1_PCA/hPSC_MEA1_PCA_meaRtools_output/hPSC_20517_MEA1_STTC.csv

@@ -0,0 +1,7 @@
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Data/PCA/hPSC_MEA1_PCA/hPSC_MEA1_PCA_meaRtools_output/hPSC_20517_MEA1_bursts_per_min.csv

@@ -0,0 +1,7 @@
+"well","treatment","divDIV21","divDIV24","divDIV28"
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Data/PCA/hPSC_MEA1_PCA/hPSC_MEA1_PCA_meaRtools_output/hPSC_20517_MEA1_mean_dur.csv

@@ -0,0 +1,7 @@
+"well","treatment","divDIV21","divDIV24","divDIV28"
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Data/PCA/hPSC_MEA1_PCA/hPSC_MEA1_PCA_meaRtools_output/hPSC_20517_MEA1_mean_freq_in_burst.csv

@@ -0,0 +1,7 @@
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Data/PCA/hPSC_MEA1_PCA/hPSC_MEA1_PCA_meaRtools_output/hPSC_20517_MEA1_mean_spikes_in_burst.csv

@@ -0,0 +1,7 @@
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+"C4","NoTreatment","16.428","27.957","22.481"

Data/PCA/hPSC_MEA1_PCA/hPSC_MEA1_PCA_meaRtools_output/hPSC_20517_MEA1_meanfiringrate_by_active_electordes.csv

@@ -0,0 +1,7 @@
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Data/PCA/hPSC_MEA1_PCA/hPSC_MEA1_PCA_meaRtools_output/hPSC_20517_MEA1_nae.csv

@@ -0,0 +1,7 @@
+"well","treatment","divDIV21","divDIV24","divDIV28"
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Data/PCA/hPSC_MEA1_PCA/hPSC_MEA1_PCA_meaRtools_output/hPSC_20517_MEA1_per_spikes_in_burst.csv

@@ -0,0 +1,7 @@
+"well","treatment","divDIV21","divDIV24","divDIV28"
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+"C4","NoTreatment","66.819","74.957","66.649"

Data/hPSC_MEA1/hPSC_MEA1_meaRtools_output/hPSC_20517_MEA1_STTC.csv

@@ -0,0 +1,7 @@
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Data/hPSC_MEA1/hPSC_MEA1_meaRtools_output/hPSC_20517_MEA1_bursts_per_min.csv

@@ -0,0 +1,7 @@
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Data/hPSC_MEA1/hPSC_MEA1_meaRtools_output/hPSC_20517_MEA1_mean_dur.csv

@@ -0,0 +1,7 @@
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Data/hPSC_MEA1/hPSC_MEA1_meaRtools_output/hPSC_20517_MEA1_mean_freq_in_burst.csv

@@ -0,0 +1,7 @@
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Data/hPSC_MEA1/hPSC_MEA1_meaRtools_output/hPSC_20517_MEA1_mean_spikes_in_burst.csv

@@ -0,0 +1,7 @@
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Data/hPSC_MEA1/hPSC_MEA1_meaRtools_output/hPSC_20517_MEA1_meanfiringrate_by_active_electordes.csv

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Data/hPSC_MEA1/hPSC_MEA1_meaRtools_output/hPSC_20517_MEA1_nae.csv

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Data/hPSC_MEA1/hPSC_MEA1_meaRtools_output/hPSC_20517_MEA1_per_spikes_in_burst.csv

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MEMO.h5

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