The cortex contains multiple types of excitatory neuron, differentiated primarily by their layer of residence. We recorded from neuronal populations in the mouse visual cortex using 2-photon calcium imaging or Neuropixels probes, and found that excitatory neurons in layer 2/3 (L2/3) and layer 5 (L5) differ in their encoding of visual vs. nonvisual signals, with L2/3 more strongly modulated by visual stimuli and L5 more strongly modulated by movement. Movement has opposite effects on population synchrony in the two layers, desynchronizing L2/3 by abolishing spontaneous population oscillations, and synchronizing L5, where excitatory cells are less entrained by oscillation and more strongly correlated with movement itself. Spontaneous activity is lower-dimensional in L2/3 than L5, with L2/3 population activity dominated by a single dimension of overlap between spontaneous and stimulus-evoked subspaces. We conclude that the population code of in different layers of the visual cortex differentially balances visual and non-visual signals. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, 185861, 110120, 227065, 205093, 204915 European Research Council, 101097874 European Molecular Biology Organization, 740-2019

Electrophysiology has proven invaluable to record neural activity, and the development of Neuropixels probes dramatically increased the number of recorded neurons. These probes are often implanted acutely, but acute recordings cannot be performed in freely moving animals and the recorded neurons cannot be tracked across days. To study key behaviors such as navigation, learning, and memory formation, the probes must be implanted chronically. An ideal chronic implant should (1) allow stable recordings of neurons for weeks; (2) allow reuse of the probes after explantation; (3) be light enough for use in mice. Here, we present the "Apollo Implant", an open-source and editable device that meets these criteria and accommodates up to two Neuropixels 1.0 or 2.0 probes. The implant comprises a "payload" module which is attached to the probe and is recoverable, and a "docking" module which is cemented to the skull. The design is adjustable, making it easy to change the distance between probes, the angle of insertion, and the depth of insertion. We tested the implant across eight labs in head-fixed mice, freely moving mice, and freely moving rats. The number of neurons recorded across days was stable, even after repeated implantations of the same probe. The Apollo implant provides an inexpensive, lightweight, and flexible solution for reusable chronic Neuropixels recordings.

Neural activity spans multiple time scales, from milliseconds to months. Its evolution can be recorded with chronic high-density arrays such as Neuropixels probes, which can measure each spike at tens of sites and record hundreds of neurons. These probes produce vast amounts of data that require different approaches for tracking neurons across recordings. Here, to meet this need, we developed UnitMatch, a pipeline that operates after spike sorting, based only on each unit's average spike waveform. We tested UnitMatch in Neuropixels recordings from the mouse brain, where it tracked neurons across weeks. Across the brain, neurons had distinctive inter-spike interval distributions. Their correlations with other neurons remained stable over weeks. In the visual cortex, the neurons' selectivity for visual stimuli remained similarly stable. In the striatum, however, neuronal responses changed across days during learning of a task. UnitMatch is thus a promising tool to reveal both invariance and plasticity in neural activity across days. UnitMatch tracks neurons in electrophysiological recordings across multiple recording sessions. UnitMatch relies on the spike waveform and allows tracking neurons even when their functional properties change such as during memory formation.

The brain can combine auditory and visual information to localize objects. However, the cortical substrates underlying audiovisual integration remain uncertain. Here, we show that mouse frontal cortex combines auditory and visual evidence; that this combination is additive, mirroring behavior; and that it evolves with learning. We trained mice in an audiovisual localization task. Inactivating frontal cortex impaired responses to either sensory modality, while inactivating visual or parietal cortex affected only visual stimuli. Recordings from >14,000 neurons indicated that after task learning, activity in the anterior part of frontal area MOs (secondary motor cortex) additively encodes visual and auditory signals, consistent with the mice's behavioral strategy. An accumulator model applied to these sensory representations reproduced the observed choices and reaction times. These results suggest that frontal cortex adapts through learning to combine evidence across sensory cortices, providing a signal that is transformed into a binary decision by a downstream accumulator.

To interpret the world and make accurate perceptual decisions, the brain must combine information across sensory modalities. For instance, it must combine vision and hearing to localize objects based on their image and sound. Probability theory suggests that evidence from multiple independent cues should be combined additively, but it is unclear whether mice and other mammals do this, and the cortical substrates of multisensory integration are uncertain. Here we show that to localize a stimulus, mice combine auditory and visual spatial cues additively, a computation supported by unisensory processing in auditory and visual cortex and additive multisensory integration in frontal cortex. We developed an audiovisual localization task where mice turn a wheel to indicate the joint position of an image and a sound. Scanning optogenetic inactivation of dorsal cortex showed that auditory and visual areas contribute unisensory information, whereas frontal cortex (secondary motor area, MOs) contributes multisensory information to the decision of the mouse. Neuropixels recordings of >10,000 neurons in frontal cortex indicated that neural activity in MOs reflects an additive combination of visual and auditory signals. An accumulator model applied to the sensory representations of MOs neurons reproduced behaviourally observed choices and reaction times. This suggests that MOs integrates information from multiple sensory cortices, providing a signal that is then transformed into a binary decision by a downstream accumulator.

Summary To make accurate perceptual decisions, the brain often combines information across sensory modalities. For instance, localizing objects by integrating their image and sound. However, the cortical substrates underlying this audiovisual integration remain uncertain. Here, we show that mouse frontal cortex combines auditory and visual evidence; that this combination is additive, mirroring behavior; and that it evolves with learning. Scanning optogenetic inactivation demonstrated that inactivating frontal cortex impaired choices based on either sensory modality. Recordings from >10,000 neurons indicated that after task learning, activity in frontal area MOs (secondary motor cortex) encodes an additive combination of visual and auditory signals, consistent with the mice’s behavioral strategy. An accumulator model applied to these sensory representations reproduced both the observed choices and reaction times. These results indicate that frontal cortex adapts through learning to combine evidence across sensory cortices, providing a signal that is transformed into a binary decision by a downstream accumulator.

Transgenic mouse lines are invaluable tools for neuroscience but, as with any technique, care must be taken to ensure that the tool itself does not unduly affect the system under study. Here we report aberrant electrical activity, similar to interictal spikes, and accompanying fluorescence events in some genotypes of transgenic mice expressing GCaMP6 genetically encoded calcium sensors. These epileptiform events have been observed particularly, but not exclusively, in mice with Emx1-Cre and Ai93 transgenes, of either sex, across multiple laboratories. The events occur at >0.1 Hz, are very large in amplitude (>1.0 mV local field potentials, >10% df/f widefield imaging signals), and typically cover large regions of cortex. Many properties of neuronal responses and behavior seem normal despite these events, although rare subjects exhibit overt generalized seizures. The underlying mechanisms of this phenomenon remain unclear, but we speculate about possible causes on the basis of diverse observations. We encourage researchers to be aware of these activity patterns while interpreting neuronal recordings from affected mouse lines and when considering which lines to study.