Dual Recordings #72
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Hi Peter I usually record two different regions in total 128 channles (Cortex H3 probe = 64 channels, and Thalamus H5/E1 probe =64 channels). As far as i know Cell explorer reads the "rez.mat" for kilosort data, as i have two rez.mat files (one per structure) i dont know how to provide this information in the Session-gui. is it possible to calculate the conectivity graph between two different regions recorded with two different probes with CellExplorer? Best Jesus |
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Replies: 8 comments 12 replies
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Hi Jesus Are the two regions recorded in the same raw binary file? If so I would create one channelmap for both probes. In Kilosort you can define the two probe layouts as a single channelmap. Check our Kilosortwrapper for examples: https://github.com/petersenpeter/KilosortWrapper In general, CellExplorer operates with one spikes struct. So if you have two rez files, what you could do is import them separately into two spikes structs, and then merge the spikes structs into one, before running CellExplorer or the detection of the monosynaptic connections. You would need to write a script for merging the spikes structs yourself. |
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Hi Peter thanks for your fast reply I didnt explore these scripts yet. I tried first to use a bin file with 128 channels and I then created a channel map with 2 probes H5 Cortex and E1 thalamus but it seems Cell Explorer is considering both as the same Probe. https://drive.google.com/file/d/1cGCltNQNDPtD2P2UlOZ5QOh7fSniMjfM/view?usp=sharing %channel map looking like this
however when i run CellExplorer i get the following trilatered position Is there an additional parameter that i need to set up in the session-gui before running the Cell_metrics gui? Thank you very much in advance |
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Your channel map looks fine, except for the large offset between the two probes. Perhaps you need to define the bad channels (e.g. noisy or floating channels)? They can skew the estimation of cell's spatial locations... they are stored in: session.channelTags.Bad.channels, but you can also add them via the GUI. Otherwise, could you try to delete all the files generated by CellExplorer (session, spikes, cell metrics, and so on), and rerun the ProcessCellMetrics? |
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Hi Jesus. Could you share the session with me? I can much better troubleshoot this way. |
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Could you share your binary file with me as well? |
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Hi Jesus I created an updated session struct, where I added channel 15 as a Bad channel (It has huge artifacts), and created 4 electrode groups instead of one. Check it out. Now the cells are correctly projected on your shanks/probes. There are two cells that are shown in the middle of the probes, but I don't think they are real neurons and appear more to be related to noise artifacts. The trilaterated position is calculated in this script: https://github.com/petersenpeter/CellExplorer/blob/40e7c11d531f1673bf569d34d5e7236c95ec3f6f/calc_CellMetrics/trilat.m It uses the spike amplitudes from the channels with the largest amplitudes (default up to 16 channels) and estimates the position using trilateration (check the code). The connectivity graph is estimated from the monosynaptic connections. It does not know the strength of the connections, purely based on the binary connectivity matrix. I am using Matlab's built-in plot: https://se.mathworks.com/help/matlab/ref/graph.conncomp.html |
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Hi Jesus
Sorry for the late reply. I had a chance to look at your data today. Are you doing stimulation - it seems like you have some large artifacts?
I created an updated session struct, where I added channel 15 as a Bad channel (It has huge artifacts), and created 4 electrode groups instead of one. Check it out. Now the cells are correctly projected on your shanks/probes. There are two cells that are shown in the middle of the probes, but I don't think they are real neurons and appear more to be related to noise artifacts.
temp_wh.session.mat.zip
The trilaterated position is calculated in this script: https://github.com/petersenpeter/CellExplorer/blob/40e7c11d531f1673bf569d34d5e7236c95e…