setGainCalibration: CSV_READ_ERROR

[paolahydra]

Hi,

I am using:
OneBox
Neuropixel 2.0 probe
OpenEphys GUI v0.6.7
Neuropix-PXI 0.7.1

In the console, I receive this message:

[open-ephys] OneBox initialized on slot 16
[open-ephys] Updating settings for 1 probes.
[open-ephys] Updating queue for probe Neuropixels 2.0 - Multishank
[open-ephys] Initialized, applying probe settings...
[open-ephys] Applying probe settings for Neuropixels 2.0 - Multishank
[open-ephys] Setting reference for slot: 16 port: 1 dock: 1 to Ext
[open-ephys] ERROR setGainCalibration: CSV_READ_ERROR
[open-ephys] Wrote configuration

Is this something I should be concerned about?

The calibration files are in C:\ProgramData\Open Ephys\CalibrationInfo<probe_serial_number> and are correctly located by OpenEphys, meaning that I do not receive any warnings (as I would if I removed the files).
Also, the calibration files are per se OK -- I have used the same probe and file already in another setup with Neuropix-PXI.

Thank you for your help.
Paola

[jsiegle]

We haven't seen this error before, but I think it does indicate the calibration is not being set. Based on the Neuropixels API documentation, this error indicates a "parsing error occurred while reading a malformed CSV file." Can you try opening the CSV file in Excel or some other spreadsheet software to make sure it is valid?

[paolahydra]

I did open it, and it seems perfectly valid.
I even tried adding a comma after the serial number in the first row, to no avail.

22420007294_gainCalValues.csv

[paolahydra]

Hi Josh,

Here is what I learned.

Somehow, the NPX1 gain CSV files have 16 measurements for each channel, whereas the NPX2 gain files only have one measurement per channel.
When I connected a Neuropixel 1 to my OneBox, I got no CSV parsing error.
Then, I duplicated the gain value 16 times in the NPX2 CSV file, and this time, I got no error.

I do not get the same error in my other setup (NPX-PXIe, OpenEphys GUI v0.6.7, Neuropix-PXI 0.6.4), which is not running the latest PXIe firmware version (if it helps, I can send you which firmware version I have).

---

Do you agree that it is reasonable to duplicate values in the NPX2 CSV file temporarily until this issue gets fixed?

Thank you.
Paola

[jsiegle]

Hi Paola,

2.0 calibration files are only supposed to have one value per channel. Opening the file you shared in a text editor, I can see there is an extra break between each line. Other 2.0 calibration files I checked don't have this.

So, it's possible that duplicating the gain values ended up deleting this extra line break, so the file could be parsed correctly, and the 15 extra gain values were ignored. Also, I think the reason that the older version of the plugin didn't have this issue is that the more recent Neuropixels API is stricter about the file format.

Therefore, the best course of action is to delete these extra line breaks and trying to load the file again. We will also add a warning in cases where the CSV files can't be parsed properly.

[paolahydra]

Thanks Josh.
That did it. I fixed all my files!
Paola