Biology subjects

Bassler, M.

Publications and source records attributed to Bassler, M..

4 recordsLinked to original sources

bioRxiv2026

Neuroline: an integrated modular pipeline for FAIR multimodal neurophysiology data processing

The adoption of FAIR principles for code and data sharing in systems neuroscience is hindered by the size and diversity of datasets, the multitude of data formats and the complexity of analysis workflows. These challenges have led to the development of various data standards and modality-specific processing and analysis tools. However, it remains difficult to integrate the diverse processed data streams originating from state-of-the-art neurophysiology experiments into a common format, which is crucial for cross-modal analyses and open, FAIR sharing of data. To address this, we developed Neuroline, a Python package for processing neurophysiology data (electrophysiology, optical imaging, and behaviour) that combines multimodal integration, modularity, and standardised output within a single pipeline. It leverages established packages and consolidates the resulting processed data into the standardised Neurodata Without Borders (NWB) format. Neuroline provides a unified interface while preserving flexibility and extensibility. Here we describe the implementation and challenges of a pipeline capable of integrating different types of neuroscientific data and packages. Finally, we address how Neuroline contributes to the sustainability and accessibility of neuroscience data and software.

neuroscience↗

bioRxiv2026

Behavioral arousal organizes visual cortical population micro-states across the sleep-wake cycle

Brain states are conventionally defined as discrete categories, such as wakefulness, NREM sleep and REM sleep. Yet, whether these labels fully capture the organization of cortical population dynamics remains unclear. Using large-field-of-view two-photon calcium imaging of layer II/III pyramidal neurons in mouse primary visual cortex (V1), we show that population activity organizes into recurring micro-states that span conventional sleep-wake boundaries. A Hidden Markov Model fitted independently of behavioral state labels identified temporally stable micro-states with structured transition pathways. Micro-state organization was more strongly aligned with a continuous behavioral arousal axis, indexed by pupil diameter and orofacial motion, than with discrete NREM-wake categories, a relationship confirmed by mediation analysis. At the circuit level, two spatially intermingled but functionally opposing neuronal ensembles tracked this arousal axis in opposite directions. These findings establish behavioral arousal, rather than discrete wake-sleep state, as the primary organizing dimension of V1 population dynamics.

neuroscience↗

bioRxiv2026

Selective binocular integration in mouse visual cortex: binocular but not monocular neurons respond distinctly to congruent stimuli

Even though binocular integration is a foremost example of integrative computations in the brain, it remains unknown how the visual cortex mediates it. Here, we investigated neuronal responses to binocular stimuli in layers 2/3 of mouse primary visual cortex (V1) and lateromedial (LM) area with in vivo two-photon imaging. We presented mice with three types of binocular stimuli: congruent gratings, orthogonal gratings and a flashing Mondrian pattern in binocular conflict with a grating. We looked for congruency-specific responses to the binocular stimuli, but found that most neurons responded homogeneously across stimulus types. Responses of cells with a strong monocular preference for the contralateral eye responded similarly to monocular and binocular stimulation, while responses of cells with a preference for ipsilateral stimuli showed a strong but nonspecific suppression to all binocular stimuli. Only cells without a strong monocular preference (i.e. binocular cells) exhibited linear integration of monocular responses to incongruent stimuli and binocular facilitation to congruent gratings. Responses to ipsilateral components of a binocular display were found to be poor predictors of binocular responses regardless of eye preference of individual cells. We conclude that most neuronal responses to binocular stimuli in mouse V1 & LM are uninformative about the congruency of the monocular components, with the exception of binocular cells which show either linear or supralinear integration.

neuroscience↗

bioRxiv2025

Continuous Flash Suppression responses in mouse visual cortex: stimulus laterality and anesthesia effects

We investigated whether binocularly conflicting stimuli adapted from primate binocular rivalry studies could induce binocular response suppression in mouse visual cortex. We presented binocularly conflicting stimuli adapted from the paradigm of continuous flash suppression to awake and anesthetized mice and examined neuronal responses in visual areas V1 and LM. Neurons often showed a preference for the left or right eye where a monocular grating was presented, and their responses were modulated by presenting a conflicting flashing Mondrian stimulus to the other eye. The direction of this modulation depended on whether neurons preferentially responded to contralateral or ipsilateral gratings. Responses of cells with a preference for ipsilateral gratings were suppressed during binocular conflict, while contralateral-preferring cells were less suppressed or even enhanced by binocular conflict. Binocular conflict modulation continued to occur under anesthesia, but response recovery after intermittent binocular conflict only occurred in awake mice. Responses to Mondrians were modulated by binocular conflict in a similar fashion as those to grating stimuli, which suggests that mouse binocular conflict processing exhibits a distinctive dependency on stimulus laterality over other stimulus features. Finally, a canonical binocular rivalry model could be successfully fitted to our data but lacked sufficient competitive inhibition and adaptation strength to create oscillatory activity under binocular conflict.

neuroscience↗