Understanding vis_data dictionary

[RejwanSalih]

Hi Jingyi,

First of all, thanks a lot for developing the software. Clearly a lot of work went into this!

I am trying to map NP1.0 recorded neurons to anatomical location. For each neuron I have the peak channel, and I'm using the herbs output data my colleague provided to figure out where that channel was. I'm playing with the data output and have plotted the trajectory of the probe along with the channel locations:

However, I'm struggling to figure out the data structure. I have narrowed it down to 'vis_data', which contains 4 entries with keys of '0' up to '3':

Now, these structures also contain "sites", which I thought was the channel IDs starting from 1 at the tip. However, only two of the four site arrays are unique; they are duplicated between two columns. I show an example here:

Am I missing something fundamental? Any help would be appreciated!

Thanks again for this software!

Rejwan

[RejwanSalih]

The only idea I have is that these 4 "sites" arrays should start from 1, 2, 3, and 4, and perhaps there is a bug in the code in that regard. If that's the case, how do I know which should be 1 vs 2 (and 3 vs 4), as the probe could be flipped and I have no way of knowing currently.

[JingyiGF]

Hi,
In case you did not read the tutorial about probes https://github.com/JingyiGF/HERBS/blob/main/Tutorial/Probe_Related/1-Important_to_know_before_you_start.md.

The vis_data is for visulisation in HERBS used to illustrate in "Probe information window". It is not related to actually voxels in atlas.

If you want to get the actually location related to atlas, you should check site_vox, or sites_loc_b, which is 3D locs related to Bregma.

If you don't know how the probe was handled while doing surgeries, I suggest to turn on "Merge sites" button.

Let me know if anything is not clear.