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2D MEA Probe creation
Describe the issue:
I browsed through the previous thread regarding 2D MEA, and I'd like to know how to create an array for an electrode up to 26400. The MEA has 26400 electrodes, but only up to 1024 channels are used simultaneously for recording. Should I create an array for all electrodes and then specify the channels to be recorded, or should I only create an array based on the physical information of these 1024 channels?
The probe file you provide to Kilosort should only include information about the channels that you actually recorded data from.
Alright, my electrode spacing is 87.5 um. How should I set the template parameters to match my probe? I used dim and dimx as 175, but they are aligned neatly on the x-axis while there is a deviation on the y-axis.
These are my parameter settings.
This is the probe I'm using. 19531_2.zip
Thanks, that was a bug. There was some code forcing the y-positions for the templates to be integers, which I guess hadn't come up until now. You can pull the latest changes to get the fix if you installed from source, otherwise I'll add it to pip later today after working on some other changes.
Looking forward to later updates! I encountered another question. Why is the x-axis aligned after setting dim and dimx to 175, but the y-axis is offset, and the electrode spacing is 87.5um. And when I set the dim to 350, it's good to align my y-axis with half the density.
Vertical spacing was set based on dmin // 2 (floor division, i.e. rounded to an integer) while horizontal spacing was set by dminx / 2. So for dmin = 350 they're placed vertically every 175um, but for dmin = 175 they're placed every 87um instead of 87.5, which is why they were aligned at the bottom of the probe and then the alignment got worse going up. Now it will use dmin / 2.
Oh, I got it! What can I do to better match my probe? Can I try to modify the code?
You just need to install from source to get the latest code changes if you don't want to wait on a new pip version. There are instructions for that at the bottom of the readme.