Multi-day Neuron Tracking in High Density Electrophysiology Recordings using EMD

Reviewer #1 (Public Review):

The brain's code is not static. Neuronal activity patterns change as a result of learning, aging, and disease. Reliable tracking of activity from individual neurons across long time periods would enable detailed studies of these important dynamics. For this reason, the authors' efforts to track electrophysiological activity across days without relying on matching neural receptive fields (which can change due to learning, aging, and disease) are very important.

By utilizing the tightly-spaced electrodes on Neuropixels probes, they are able to measure the physical distance and the waveform shape 'distance' between sorted units recorded on different days. To tune the matching algorithm and validate the results, they used the visual receptive fields of neurons in the mouse visual cortex (which tend to change little over time) as ground truth. Their approach performs quite well, with a high proportion of neurons accurately matched across multiple weeks. This suggests that the method may be useable in other cases where the receptive fields can't be used as ground truth to validate the tracking. This potential extendibility to tougher applications is where this approach holds the most promise.

The main caveat (and disappointment) is that this paper does not address generalizability to other experimental conditions. Because it only looks at one brain area (visual cortex), in one species (mouse), using one type of spike sorter (Kilosort), and one type of behavioral prep (head-fixed), it is not clear if this approach is overfit to those conditions or if it will perform equally well in other conditions. Most importantly, in brain areas where neuronal receptive fields are more dynamic and can't be used as a ground truth diagnostic, it isn't clear how to apply the technique outlined in this study, since many of the parameters are tuned to a very specific set of conditions using visual receptive fields as ground truth.

Reviewer #2 (Public Review):

The manuscript presents a method for tracking neurons recorded with neuropixels across days, based on the matching of cells' spatial layouts and spike waveforms at the population level. The method is tested on neuropixel recordings of the visual cortex carried over 47 days, with the similarity in visual receptive fields used to verify the matches in cell identity.

This is an important tool as electrophysiological recordings have been notoriously limited in terms of tracking individual neuron's fate over time, unlike imaging approaches. The method is generally sound and properly tested but I think some clarifications would be helpful regarding the implementation of the method and some of the results.

1. Page 6: I am not sure I understand the point of the imposed drift and how the value of 12µm is chosen.
   Is it that various values of imposed drift are tried, the EMDs computed to produce histograms as in Fig2c, values of rigid drifts estimated based on the histogram modes, and then the value associated with minimum cost selected? The corresponding manuscript section would need some clarification regarding this aspect.

2. The EMD is based on the linear sum, with identical weight, of cell distance and waveform similarity measures. How performance is affected by using a different weighting of the 2 measures (for instance, using only cell distance and no waveform similarity)? It is common that spike waveforms associated with a given neuron appear differently on different channels of silicon probes (i.e. the spike waveform changes depending on the position of recording sites relative to the neuron), so I wonder if that feature is helping or potentially impeding the tracking.

3. Fig.5: I assume the dots represent time gaps for which cell tracking is estimated. The 3 different groups of colors correspond to the 3 mice used. For a given mouse, I would expect to always see 3 dots (for ref, putative, and mixed) for a given tracking gap. However, for mouse AL036 for instance, at a tracking duration of 8 days, a dot is visible for mixed but not for ref and putative. How come this is happening?

4. Matched visual responses are measured by the sum of the correlation of visual fingerprints, which are vectors of cells' average firing rate across visual stimuli, and the correlation of PSTHs, which are implemented over all visual stimuli combined. I believe that some information is lost from combining all stimuli in the implementation of PSTHs (assuming that PSTHs show specificity to individual visual stimuli). The authors might consider, as an alternative measure of matched visual responses, a correlation of the vector concatenations of all stimulus PSTHs. Such a simpler measure would contain both visual fingerprint and PSTH information, and would not lose the information of PSTH specificity across visual stimuli.