cajal / microns_phase3_nda Goto Github PK

First, thanks a lot for making your datasets publicly available!

I had a brief look into the calcium imaging data set, and I have a very short and specific question: The data set includes the "raw fluorescence", as you write in the Readme:

nda.Fluorescence: Records the raw fluorescence traces for each segmented mask

However, there are also negative values, and the range of the traces seems to be closer to dF/F, rather than raw fluorescence values from the microscope. Could you clarify whether the nda.Fluorescence is raw fluorescence or "raw" dF/F ?

Best wishes,
Peter

When I try to retrieve the pupil trace of the same session and scan_idx (even the same unit_id but that shouldn't matter iiuc.) as I see in the notebook I get a vector filled with nans. Actually I didn't find any scan that had a non-nan pupil radius. What am I doing wrong?

When running the notebooks, on from phase3 import nda, func, utils I am prompted to enter my DataJoint username and password. I have made an account and am able to log into it on the datajoint website.
However, when enter my username and password I get the error (2003, "Can't connect to MySQL server on 'localhost' ([Errno 111] Connection refused)") .
I have tried logging in both with my username and my email many times. I have tried on a cluster with ssh port forwarding to my laptop (to view the notebook), as well as on my own laptop running ubuntu 22.02 .

What could be causing this?