Temporal Dynamics of Cortical State Plasticity Following Adult Vision Loss

Reviewer #1 (Public review):

Summary:

In this study, the authors perform longitudinal mesoscale calcium imaging of visual and other cortical areas following binocular enucleation (blinding through the removal of the eyes) in adult mice. The study is observational and exploratory, and analyzes changes in the frequency distribution of calcium signals during locomotion and quiescence as a function of time after enucleation. They also analyze correlations between calcium signals in different brain regions to ask how apparent connectivity between regions changes over time. The main conclusions are (1) that there are multiple timescales of plasticity; (2) that the coupling between locomotion and activity in visual areas flips sign after enucleation, and (3) that correlations between brain areas are modulated by this long-lasting plasticity. Overall, the data are likely to be useful to researchers studying the impact of injury and catastrophic loss of sensory inputs on brain reorganization, but it is hard to draw firm conclusions from the observations provided beyond the very general conclusions listed above.

Strengths:

(1) The longitudinal imaging of multiple brain areas simultaneously allows the investigators to follow plastic changes in the same animals over time, to address questions about how apparent connectivity and brain state modulation unfold after injury.

(2) The data suggesting a flip in sign of the coupling between movement and "activity" in visual areas is interesting and potentially novel.

Weaknesses:

(1) The mesoscale imaging has limitations. In particular, the authors use words/phrases such as "activity" and "functional connectivity" without ever discussing what the measures they provide with this approach (frequency distribution of summed calcium fluctuations, and the correlation between this measure across brain areas) actually mean, or how they approximate spike-based measures or cellular-resolution Ca signals. The manuscript would benefit from an in-depth discussion of these limitations.

(2) In general, the figures are difficult to follow. In many cases, what is being plotted is hard to extract without a lot of work, and metrics are not well-justified. For example, they calculate the R value between movement power and spectral power of the Ca signal to quantify changes across time in the coupling between movement and activity (Figure 2). But from the example given, this does not look like a continuous relationship, and though R values are significant its not clear that this correlation is a good way of quantifying the change in sign they attempt to document. Figure 7 is impossible to read, and areas quantified are not indicated. The reader should not have to work this hard to figure out what they are plotting.

(3) It would be reassuring to rule out an effect of repeated imaging on the metrics they describe here. Longitudinal imaging of the same duration without enucleation would be the best control. Alternatively, they do have multiple baseline measurements that they collapse into one value in most of their plots.

(4) The discussion is very long. They spend a lot of time trying to relate their findings to the larger literature on visual deprivation, but because of differences in paradigms (enucleation, laser ablation, visual deprivation, binocular vs monocular) and differences in measures (see point 1), it's hard to draw conclusions. In my view, the manuscript would benefit from less speculation about plasticity mechanisms and more discussion of the strengths and weaknesses of their approach.

Reviewer #2 (Public review):

Summary:

This study uses cortex-wide mesoscopic calcium imaging to investigate how adult vision loss induced by bilateral enucleation alters spontaneous cortical activity across behavioral states, including quiescence, locomotion, and anesthesia. The authors perform longitudinal imaging over two time scales, spanning days to weeks and weeks to months after enucleation, enabling them to track the changes of cortical reorganization.

The main findings are that oscillatory activity in V1 undergoes a strong reversal in its relationship to behavioral state. Before enucleation, V1 activity is positively correlated with locomotion and negatively correlated with quiescence, whereas after vision loss, this pattern reverses. State-transition dynamics are similarly altered: locomotion onset shows reduced V1 activation, while cessation of locomotion is associated with increased activity after enucleation, while it caused suppression during baseline. In addition, the authors report an increase in slow-wave (0.1-4 Hz) activity in V1 after enucleation, starting in the first week and lasting over many weeks. Although these effects show partial recovery over time, many abnormalities persist for weeks to months.

At the network level, the study reveals altered large-scale cortical organization, including reduced functional connectivity involving V1 that appears to remain impaired.

Strengths:

Overall, the work provides a thorough characterization of how adult vision loss reshapes cortical dynamics, particularly with respect to behavioral-state modulation.

Weaknesses:

However, there is also a lack of clarity due to the way the data are presented. Moreover, the study remains largely descriptive, as it does not address the mechanisms underlying these changes or their functional significance, making it difficult to interpret the broader implications of the observed cortical reorganization.

Reviewer #3 (Public review):

Summary:

The authors track cortical activity across the dorsal cortex of head-fixed mice for up to ten weeks following bilateral eye removal, asking how the cortex reorganizes over an extended period after vision loss. They report a rapid and long-lasting reversal of the normal relationship between movement and visual cortex activity, together with a delayed, weeks-long window of enhanced slow-wave activity during rest and a persistent reorganization of large-scale cortical correlations.

Strengths:

The longitudinal scope is the work's strength. Tracking the same animals over a ten-week window after sensory loss is technically demanding and rarely done, and it yields a temporal picture that short studies cannot provide. The observation that the movement-related activation of the visual cortex inverts within a day and only partially recovers over weeks is striking and has not been documented at this timescale. The analysis is internally consistent across two protocols (short- and long-term) and frames the changes by behavioral state, focusing on rest versus movement. This is a useful analysis that the field has not systematically applied to studies of deprivation.

Weaknesses:

The manipulation is unusually severe: removing both eyes eliminates patterned vision, non-image-forming light input, and all residual retinal signals abruptly and irreversibly, in contrast to the milder and often reversible manipulations the discussion draws on. Without a sham-surgery control, the early effects cannot be cleanly separated from the surgery itself.

The language of "plasticity" runs ahead of what the data actually measure, since the study quantifies spontaneous activity and pairwise correlations but does not assess receptive fields, evoked responses, synaptic changes, or the causal manipulation of any candidate circuit. The discussion nevertheless attributes findings to specific interneuron circuits, molecular pathways, and thalamocortical reorganization, none of which are tested in this study.

The imaging method also constrains what can be claimed: widefield calcium signals are dominated by superficial-layer and excitatory output and cannot resolve the cell-type-specific mechanisms invoked in the discussion. Because the key findings lie in the low-frequency band where vascular contamination is greatest, the hemodynamic correction, particularly in the deprived state, where vascular tone itself may be altered, deserves more validation than it currently receives.

Finally, the presentation relies heavily on group-level heatmaps in the main figures, with raw traces, spectrograms, and per-animal trajectories at the key inflection points (day 1, week 1, week 10) largely absent. This makes it difficult to judge whether the reported patterns are coherent across animals.