Biology subjects

Aymanns, F.

Publications and source records attributed to Aymanns, F..

4 recordsLinked to original sources

bioRxiv2026

Real-Time Multi-Position and Multi-ROI Tracking with LiLiTTool for Smart Light-Sheet Microscopy in Growing Samples

Long-term live imaging of growing samples with light-sheet fluorescence microscopy provides unique insights into development, but morphogenesis often displaces features of interest outside the microscopes field of view (FOV), calling for automated methods to track these features and update the microscopes FOV in real time. Existing solutions, which typically rely on local or global intensity distributions, struggle to follow specific features robustly throughout morphogenesis, leading to truncated or incomplete datasets. Here, we present a light-sheet live tracking tool (LiLiTTool) that maintains user-defined regions of interest (ROI) within the FOV throughout extended imaging sessions. LiLiTTool uses Cotracker3, a state-of-the art deep learning-based motion predictor, augmented by sensor fusion with a trained object-detector. This enables robust compensation for drift, rotation, and deformation during morphogenesis, while meeting the timing constraints of live acquisition. We validated LiLiTool by integrating with the Viventis LS1 microscope, achieving sub-second processing and stable tracking of growing zebrafish embryos over many hours. LiLiTTool supports multi-ROI tracking in 3D, enabling simultaneous monitoring of multiple features within the same embryo and in multiple embryos during a single acquisition. LiLiTTool is modular and openly available on GitHub and as a napari plugin for post-acquisition tracking. By enabling precise, adaptive, and scalable real-time imaging, LiLiTTool advances smart microscopy approaches and provides the developmental biology community with a practical tool for capturing reliable spatio-temporal information in growing embryos or other morphogenetic systems.

developmental biology↗

bioRxiv2022

Descending neuron population dynamics during odor-evoked and spontaneous limb-dependent behaviors

Deciphering how the brain regulates motor circuits to control complex behaviors is an important, long-standing challenge in neuroscience. In the fly, Drosophila melanogaster, this is accomplished by a population of [~] 1100 descending neurons (DNs). Activating only a few DNs is known to be sufficient to drive complex behaviors like walking and grooming. However, what additional role the larger population of DNs plays during natural behaviors remains largely unknown. For example, they may modulate core behavioral commands, or comprise parallel pathways that are engaged depending on sensory context. We evaluated these possibilities by recording populations of nearly 100 DNs in individual tethered flies while they generated limb-dependent behaviors. We found that the largest fraction of recorded DNs encode walking while fewer are active during head grooming and resting. A large fraction of walk-encoding DNs encode turning and far fewer weakly encode speed. Although odor context does not determine which behavior-encoding DNs are recruited, a few DNs encode odors rather than behaviors. Lastly, we illustrate how one can identify individual neurons from DN population recordings by analyzing their spatial, functional, and morphological properties. These results set the stage for a comprehensive, population-level understanding of how the brains descending signals regulate complex motor behaviors.

neuroscience↗

bioRxiv2022

Ascending neurons convey behavioral state to integrative sensory and action selection centers in the brain

Knowledge of ones own behavioral state--whether one is walking, grooming, or resting--is critical for contextualizing sensory cues including interpreting visual motion and tracking odor sources. Additionally, awareness of ones own posture is important to avoid initiating destabilizing or physically impossible actions. Ascending neurons (ANs), interneurons in the vertebrate spinal cord or insect ventral nerve cord (VNC) that project to the brain, may provide such high-fidelity behavioral state signals. However, little is known about what ANs encode and where they convey signals in any brain. To address this gap, we performed a large-scale functional screen of AN movement encoding, brain targeting, and motor system patterning in the adult fly, Drosophila melanogaster. Using a new library of AN sparse driver lines, we measured the functional properties of 247 genetically-identifiable ANs by performing two-photon microscopy recordings of neural activity in tethered, behaving flies. Quantitative, deep network-based neural and behavioral analyses revealed that ANs nearly exclusively encode high-level behaviors--primarily walking as well as resting and grooming--rather than low-level joint or limb movements. ANs that convey self-motion--resting, walking, and responses to gust-like puff stimuli--project to the brains anterior ventrolateral protocerebrum (AVLP), a multimodal, integrative sensory hub, while those that encode discrete actions--eye grooming, turning, and proboscis extension--project to the brains gnathal ganglion (GNG), a locus for action selection. The structure and polarity of AN projections within the VNC are predictive of their functional encoding and imply that ANs participate in motor computations while also relaying state signals to the brain. Illustrative of this are ANs that temporally integrate proboscis extensions over tens-of-seconds, likely through recurrent interconnectivity. Thus, in line with long-held theoretical predictions, ascending populations convey high-level behavioral state signals almost exclusively to brain regions implicated in sensory feature contextualization and action selection.

neuroscience↗

bioRxiv2021

Long-term imaging of the ventral nerve cord in behaving adult Drosophila

The dynamics and connectivity of neural circuits continuously change during an animals lifetime on timescales ranging from milliseconds to days. Therefore, to investigate how biological networks accomplish remarkable cognitive and behavioral tasks, minimally invasive methods are needed to perform repeated measurements, or perturbations of neural circuits in behaving animals across time. Such tools have been developed to investigate the brain but similar approaches are lacking for comprehensively and repeatedly recording motor circuits in behaving animals. Here we describe a suite of microfabricated technologies that enable long-term, minimally invasive optical recordings of the adult Drosophila melanogaster ventral nerve cord (VNC)--neural tissues that are functionally equivalent to the vertebrate spinal cord. These tools consist of (i) a manipulator arm that permits the insertion of (ii) a compliant implant into the thorax to expose the imaging region of interest; (iii) a numbered, transparent polymer window that encloses and provides optical access to the inside of the thorax, and (iv) a hinged remounting stage that allows gentle and repeated tethering of an implanted animal for two-photon imaging. We validate and illustrate the utility of our toolkit in several ways. First, we show that the thoracic implant and window have minimal impact on animal behavior and survival while also enabling neural recordings from individual animals across at least one month. Second, we follow the degradation of chordotonal organ mechanosensory nerve terminals in the VNC over weeks after leg amputation. Third, because our tools allow recordings of the VNC with the gut intact, we discover waves of neural population activity following ingestion of a high-concentration caffeine solution. In summary, our microfabricated toolkit makes it possible to longitudinally monitor anatomical and functional changes in premotor and motor neural circuits, and more generally opens up the long-term investigation of thoracic tissues.

neuroscience↗