Biology subjects

Baruchin, L. J.

Publications and source records attributed to Baruchin, L. J..

7 recordsLinked to original sources

bioRxiv2026

Correcting axial-motion artifacts in two-photon calcium imaging with suite2p-in-depth

Two-photon calcium imaging enables measurements of neural activity from individual neurons and their subcellular processes in awake animals. Axial brain motion can change measured fluorescence independently of neural activity and move small structures out of the imaging plane, confounding two-photon calcium measurements in behaving animals. We developed two complementary post-acquisition methods, selected according to whether the imaged structure remains detectable across the encountered depth range. When it does, z-stack correction estimates imaging depth from a separately acquired reference z-stack and uses an axial fluorescence profile specific to each neural structure to rescale fluorescence to a common reference depth. When a structure can leave a single imaging plane, volume-based z-registration reconstructs a common-depth movie from repeated acquisitions of closely spaced planes. In awake mice, both methods tracked experimentally imposed axial displacements within the sampled range, with depth-estimation root mean squared errors (RMSEs) below 1 m for z-stack correction and 0.69-1.03 m for volume-based z-registration. Correction changed fluorescence substantially for a subset of somata, with larger effects in axonal boutons. Both methods are implemented in suite2p-in-depth, a Python package that integrates with Suite2p and provides diagnostics for depth estimation, correction quality and data reliability. Together, these methods enable axial-motion artifacts to be assessed and corrected within established Suite2p workflows.

neuroscience↗

bioRxiv2025

Suite3D: Volumetric cell detection for two-photon microscopy

In two-photon imaging of neuronal activity it is increasingly common to acquire 3-dimensional volumes. However, these volumes are typically processed plane by plane, leading to uncorrected axial movement, duplicated cells across planes, reduced signal-to-noise ratio per cell, and missed cells. To overcome these limitations, we introduce Suite3D, a volumetric cell detection pipeline. Suite3D corrects for rigid and non-rigid 3D brain motion, both lateral and axial. It detects neurons using 3D correlation, improving detectability. Finally, it performs 3D segmentation, identifying cells across imaging planes. We validated Suite3D with data from conventional multi-plane microscopes and advanced volumetric microscopes, at multiple resolutions and in multiple brain regions, and with ground truth anatomical labelling. Suite3D successfully detected cells appearing on multiple imaging planes, improving cell detectability and signal quality, avoiding duplications, and running faster than a prior volumetric pipeline. Suite3D offers a powerful solution for analyzing volumetric two-photon data.

neuroscience↗

bioRxiv2023

GABAergic circuits reflect different requirements for emergent perception in postnatal mouse neocortex

Information transfer in the mammalian cerebral cortex is dependent on locally-projecting GABAergic interneuron circuits that are widely assumed to be uniform across neocortical areas. We demonstrate that this does not hold true during the highly dynamic period of postnatal life prior to the onset of active sensory exploration. During this time, a subset of interneuron defined by expression of the neuropeptide somatostatin differentially contribute to sensory-evoked activity in primary somatosensory and visual cortices. This functional divergence between the two areas is explained by differences in the composition of somatostatin interneuron subtypes and the transient circuits formed by these cells; the somatosensory circuit representing an adaptation to control early neonatal touch information. Understanding such area-dependent differences will promote our endeavours to understand the aetiology of developmental psychiatric disorders. Summary SentenceCortical circuits are adapted to the local information processing demands of the developing brain

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bioRxiv2022

Reward modulates visual responses in the superficial superior colliculus of mice

The superficial layers of the superior colliculus (SC) are highly visual and receive direct input from the retina. Nonetheless, neural activity in the superficial SC (sSC) is modulated by locomotion and pupil-linked arousal. Here we show that visual responses of neurons in the sSC are additionally modulated by reward delivered prior to the visual stimulus. We trained mice to perform a visual detection task and recorded the activity of neurons in the SC using two-photon calcium imaging and electrophysiological recordings using high-density silicone probes (Neuropixels). Neurons across all layers of the SC responded to various task events, including reward delivery. However, responses to events like licking or movements did not explain the visual response modulation by reward. Electrophysiological recordings showed that most of the reward modulation occurred in the superficial rather than the deeper layers of the SC. Neurons also exhibited modulation by pupil-linked arousal, which was independent of the reward modulation. Performance of a population decoder to detect visual stimuli improved significantly by reward modulation but not by pupil-linked arousal modulation. Our results indicate that behavioural factors other than locomotion and arousal modulate visual activity in the SC.

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bioRxiv2021

Retrosplenial cortex is necessary for spatial and non-spatial latent learning in mice

Latent learning occurs when associations are formed between stimuli in the absence of explicit reinforcement. Traditionally, latent learning in rodents has been associated with the creation internal models of space. However, increasing evidence points to roles of internal models also in non-spatial decision making. Whether the same brain structures and processes support the creation of spatially-anchored or non-spatial internal models via latent learning, is an open question. To address this question, we developed a novel operant box task that allows to test spatial and non-spatial versions of a flavour-based sensory preconditioning paradigm. We probed the role of the retrosplenial cortex, a brain area associated with spatial cognition and subjective value representation, in this task using precise, closed-loop optogenetic silencing during different task phases. We show that the retrosplenial cortex is necessary for both spatial and non-spatial latent learning in mice. We further demonstrate that the requirement of retrosplenial cortex is limited to the preconditioning phase of the task. Our results provide insight into the specific role of the retrosplenial cortex in latent learning, demonstrate that latent learning plays a general part in the creation of internal models, independent of spatial anchors, and provide a novel avenue for studying model-based decision making.

neuroscience↗

bioRxiv2021

Contribution of interneuron subtype-specific GABAergic signalling to emergent sensory processing in somatosensory whisker barrel cortex in mouse.

Mammalian neocortex is important for conscious processing of sensory information. Fundamental to this function is balanced glutamatergic and GABAergic signalling. Yet little is known about how this interaction arises in the developing forebrain despite increasing insight into early GABAergic interneuron (IN) circuits. To further study this, we assessed the contribution of specific INs to the development of sensory processing in the mouse whisker barrel cortex. Specifically we explored the role of INs in speed coding and sensory adaptation. In wild-type animals, both speed processing and adaptation were present as early as the layer 4 critical period of plasticity, and showed refinement over the period leading to active whisking onset. We then conditionally silenced action-potential-dependent GABA release in either somatostatin (SST) or vasoactive intestinal peptide (VIP) INs. These genetic manipulations influenced both spontaneous and sensory-evoked activity in an age and layer-dependent manner. Silencing SST+ INs reduced early spontaneous activity and abolished facilitation in sensory adaptation observed in control pups. In contrast, VIP+ IN silencing had an effect towards the onset of active whisking. Silencing either IN subtype had no effect on speed coding. Our results reveal how these IN subtypes differentially contribute to early sensory processing over the first few postnatal weeks.

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bioRxiv2020

Ontogeny of the VIP+ interneuron sensory-motor circuit prior to active whisking

Development of the cortical circuits for sensory-motor processing require the coordinated integration of both columnar and long-range synaptic connections. To understand how this occurs at the level of individual neurons we have explored the timeline over which vasoactive intestinal peptide (VIP)-expressing interneurons integrate into mouse somatosensory cortex. We find a distinction in emergent long-range anterior-motor and columnar glutamatergic inputs onto layer (L)2 and L3 VIP+ interneurons respectively. In parallel, VIP+ interneurons form efferent connections onto both pyramidal cells and interneurons in the immediate column in an inside-out manner. Cell-autonomous deletion of the fate-determinant transcription factor, Prox1, spares long-range anterior-motor inputs onto VIP+ interneurons, but leads to deficits in local connectivity. This imbalance in the somatosensory circuit results in altered spontaneous and sensory-evoked cortical activity in vivo. This identifies a critical role for VIP+ interneurons, and more broadly interneuron heterogeneity, in formative circuits of neocortex.

neuroscience↗