Index array element error upon entry into Step 2

[oliviapembridge]

Hi!

I’ve run into an error when running the MEA-NAP pipeline that I was hoping to get some guidance on. Strangely, this error is only occurring in one of my experiments, all my other experiments (even recordings I’ve taken back to back with these ones) are fine. The only difference I can think of is that this experiment has a few more disabled electrodes than my others.

I’ve tried several timepoints and always run into this error soon after it enters step 2:

The open figure always looks something like this:

I am recording using a 12 well plate (64 electrodes) on an axion maestro pro. I double checked to make sure that I have axion64 selected as my electrode layout. Again, I have recorded with this exact well format on this machine and have success running recordings through the pipeline, this experiment is the only one giving me issue for some reason.

Do you have any advice on how I could get this dataset through the pipeline! I am happy to provide more info on my parameters or anything else.

Thank you!

[Timothysit]

Hi! Thanks for posting this issue and sorry for the delayed response. Can you let me know whether the disabled electrodes are still in the data, or are they removed from the data? Ie. if you load up the mat file, do you still see 64 channels like here:

or are you seeing something else? And did you put any electrodes as grounded in the spreadsheet?

Best,
Tim

[oliviapembridge]

Hi Tim!

The disabled electrodes are not in the data when I load up the mat file:

However, another well from the same experiment that was unpacked at the same time (but did not have disabled electrodes) still shows 64:

I have not put anything as grounded in the spreadsheet. I usually have some disabled electrodes when I record and it has never been an issue before.

Best,
Olivia

[Timothysit]

Hi Olivia!

I have just tested an example axion file where I removed 3 electrodes from the data to replicate the 61 electrode example. I made some changes to the implicated plotNodeHeatmap function but I don't think they are directly related to the error you saw. After the fix, the recording ran through the entire pipeline with no issues. I think it will be most helpful if you can identify which particular file is causing the error, and try running the latest MEA-NAP code and see if it works, let me know how it goes!

Best,
Tim

[oliviapembridge]

Hi Tim!

I have one well that has 3 electrodes consistently disabled due to a manufacturing error. I was previously able to get some of my recordings through by removing that file! However, I now have a few time points left that still give the same error despite not having any wells remaining that have more than 1 or 2 electrodes disabled (still within the same experiment, but for some reason removing the bad well didn’t work for these).

I will try running them with the updated code and let you know! But I am not entirely positive anymore that it is because of the three disabled electrodes.

Thank you!
Olivia