Hello!
So this is the reference article that I am basing my project off of. Since the Arduino MEGA/autonomous navigation code is not working properly and I don’t yet have a replacement for the former, my mentor suggested I begin working on the cell culture-MATLAB connection instead.
What the reference article does
Before I got started replicating what they did, I first had to understand it. Anyway, here’s a nice flow chart I drew up that describes how their ‘output decoding’ works:
investigation: programs to use
I really should have written this the day of, but here’s a rough summary of my exact reasoning… In the reference article, the researchers were correlating input (stimulating the cell cultures) to exact output (spiking) from that culture. As such, what I’m looking to do is feed real-time spiking data from the cell culture into MATLAB for processing. This is where particular sets of spiking could be identified and then ‘translated’ into commands to the robot.
The NE Lab uses the MultiChannel Systems (MCS) data acquisition setup to collect data from the MEAs (multi-electrode arrays) holding our neuronal cell cultures. That means the data is read in through the MC_Rack software, which is supplemented by others built by MCS to work in the same environment. I found the MC_Rack webpage, and I began searching for ways to export data to other programs–and eventually MATLAB. For some reason, I thought I would need to do complex data analysis, so I began exploring the linked program, Neuroexplorer (NEX), where you can essentially do lots of cool analysis. It can also provide for a direct link to MATLAB, and that seemed like what I was looking for (so plan was: MC_Rack –> Neuroexplorer –> MATLAB). I then learned that our lab had NEX 4, not NEX5, the former of which cannot do spike-analysis… it assumes that any imported data will have already-sorted waveforms. So… that wasn’t useful; since the end goal was to have this run in real-time, I wanted something that took as few steps as possible and didn’t require any human intervention.
Next, I found this tool called MultiChannel Data Manager, which can ‘translate’ MC_Rack recordings into something workable with MATLAB. I even downloaded and began setting up this program, because I had some data recordings available to work with. I realized, however, that it would only really work with such imported data–so wouldn’t be useful in the long run, where my goal was real-time input. I also checked back with NEX, and it looks like that doesn’t work in real-time either (it keeps mentioning importing).
What next?
I want neuronal spiking to be transferred to and further processed in MATLAB. Since the current issue is to figure out how to process the data in real-time, my mentor suggested I look for other research articles that tackle that issue. This one here looks promising.