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igm-team / meaRtools

An R package for the Comprehensive Analysis of Neuronal Networks Recorded on Microelectrode Arrays
GNU General Public License v3.0
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data input - read_spikelist_text #50

Open Pedrodpj92 opened 5 years ago

Pedrodpj92 commented 5 years ago

Hello,

We are Pedro Del Pozo and Javier de Lucas, from University of Alcalá (Spain). We found this repository through this article:

https://www.ncbi.nlm.nih.gov/pubmed/30273353

Our research group is interested in applying some meaRtools' features. However, we have some doubts about how to adapt our own data.

We found difficulties adapting input data. For the purpose of getting used with the tool, firstly we followed the General Usage example ( https://cran.r-project.org/web/packages/meaRtools/vignettes/meaRtoolsGeneralUsage.html ), using your available data ( https://github.com/igm-team/meaRtools/tree/master/test/exampleRecording ). Everything worked fine. After that, we checked how to use any other dataset based in csv, as shown in this link:

https://cran.r-project.org/web/packages/meaRtools/vignettes/data_input.html

We are trying to adapt the data you provide to our own generic plate architecture, just to see if the package's results are the same. But we found some problems. Are there any dependencies among plate electrodes/wells positions and csv electrode labels?

Our generic plate may be generated in a similar way as this, following your examples:

demas_platelayout <- list(n_well = 48,
                          wells = unique(synthetic_wells),
                          n_well_r = 1,
                          n_well_c = 48,
                          layout = c(1, 48),
                          n_elec_r = 1,
                          n_elec_c = 16,
                          xlim = c(-100, 1700),
                          ylim = c(100, -4800),
                          spacing = 100,
                          corr_breaks = 0
)
add_plateinfo("TEST_48well", demas_platelayout)

We also do not understand perfectly the differences using read_spikelist and read_spikelist_text. May they return different data structures?

Before making a larger issue, we need to ask if our solution on "generic plate" can be adapted to this tool. If you think that those problems may be discussed by other via, such as email or what you prefer, or if you need more details, we will try our best.

Thanks for reading us, Pedro and Javier

sje30 commented 5 years ago

Thanks for your message. Do you have an example file and description of the MEA layout you are trying to use? The package was admittedly heavily optimised towards Axion recordings whereas now I am looking to widen the formats.

Pedrodpj92 commented 5 years ago

Thanks for your quick response, we explain our context:

We perform in vitro recordings with 32 electrodes MEAs. In the future we may expand the amount of electrodes. For us, identification of single units is very important, but for each recording electrode we can detect more than one neuron. Reading your paper, we understand that you assume you are recording only one neuron per electrode, or that it is not relevant if you are recording more than one.

Because of that, we had the idea of assimilating what you called electrodes to our previously identified units. In this case electrode position is not relevant for us.

So we tried out to design a "generic plate" in order to group several experiments, one per well. For each well, there is one row with all electrodes/neurons, being, for instance, 100 the total number of electrodes/neurons, some of which can be non-active in case we record less than 100 neurons. The wells are distributed in one unique column.

We are trying to adapt the data you provide to our own generic plate architecture, just to see if results are the same. Similar to next figure:

example_plate

Presuming that electrodes order in each well is not relevant to analysis results, the times file top would be:

Channel,Time E6_11,0.03936 B6_22,0.03992 D3_13,0.04096 D2_11,0.04144 B6_32,0.04208 D3_21,0.04304 D6_32,0.04392 D3_43,0.04432 D2_13,0.04464 ...

Electrode positions file would be:

"Well","Channel","x","y" "A1","A1_11",150,-50 "A1","A1_12",250,-50 "A1","A1_13",350,-50 "A1","A1_14",450,-50 "A1","A1_21",550,-50 "A1","A1_22",650,-50 "A1","A1_23",750,-50 "A1","A1_24",850,-50 "A1","A1_31",950,-50 "A1","A1_32",1050,-50 ...

The idea is that we would be able to compound several experiments in one plate for running analysis at once, as you describe both in paper and General Usage output pdf files.

sje30 commented 1 year ago

SOrry for the long delay.

If you have an example data file online with a short recording, I can take a look.