Biology subjects

Jacoby, J.

Publications and source records attributed to Jacoby, J..

3 recordsLinked to original sources

bioRxiv2026

High precision animal stereotaxis with 3D polychromic photogrammetry

Stereotaxic brain surgery is a foundational neurosurgical technique used to deliver chemical, pharmacological, or genetic material to specific brain regions, or to precisely implant electrodes and stimulators. Accurate targeting depends on reliable identification of skull landmarks, particularly bregma and lambda. Here we present a photogrammetry-based automated small animal stereotaxic platform that uses a single, freely handheld camera, such as a standard smartphone, to generate high-resolution, polychromatic 3D skull reconstructions. Because photogrammetry requires no fixed overhead hardware, the surgical field remains fully accessible for instruments, microscopes, and other equipment. The resulting color reconstructions substantially improve identification of bregma and lambda compared to monochromatic approaches, and the higher spatial resolution translates directly into improved targeting accuracy and surgical speed. The system operates by a user moving a handheld camera around the exposed skull. The platform automatically produces a detailed 3D mesh and computes stereotaxic coordinates without manual measurement. Together, these properties yield a practical, accessible yet accurate platform for automated small animal neurosurgery. We previously described a structured illumination approach in combination with a Steward platform; however, that system required a fixed projector and camera array that occupied critical surgical workspace and produced monochromatic meshes that complicated landmark identification. The photogrammetry-based method described here overcomes both limitations while retaining full compatibility with the Steward platform as a stereotaxic base.

neuroscience↗

bioRxiv2026

From vehicles to wildlife: transferable deep learning for trajectory generation

Realistic simulation of animal movement is fundamental to conservation, habitat modeling, and ecological scenario evaluation. Traditional approaches struggle to capture multi-scale trajectory dynamics, while generative deep learning for complete trajectory simulation remains largely unexplored in ecology due to data scarcity. We show that a diffusion model pre-trained on millions of vehicle GPS trajectories can be fine-tuned on hundreds of seabird central-place foraging trips to simultaneously generate ecologically realistic trajectories for five species and six breeding colonies. The fine-tuned model consistently outperforms four state-of-the-art baselines (GAN, VAE, HMM, iSSF) across movement metrics spanning step dynamics, spatial distribution, and behavioral temporality, with comparable or shorter computation times. Domain transfer reaches full performance in 35 minutes versus 7 hours from scratch, and conditioning on species and colony enables generalization to unseen combinations from as few as 10 trajectories. These results establish cross-domain transfer learning as a new paradigm for data-efficient generative animal movement modeling.

bioinformatics↗

bioRxiv2025

Altered striatal dopamine dynamics and behavior in Grin2a mutant mice, a genetic mouse model of schizophrenia

Schizophrenia (SCZ), a complex psychiatric disorder with a strong genetic basis, is thought to involve, at least in part, dopamine dysregulation in the striatum. Recent large-scale exome sequencing has identified multiple SCZ risk genes, including GRIN2A (encoding an NMDA (N-methyl-D-aspartate) receptor subunit) and AKAP11 (encoding a protein kinase A binding protein), which is also a risk gene for bipolar disorder (BD). However, the mechanisms by which these genetic risk factors perturb dopamine circuits and cause psychotic symptoms remain poorly understood. We asked how behavior, dorsomedial striatal dopamine (DA) dynamics and the activity of D1-/D2-spiny projection neurons (SPNs) were altered in Grin2a and Akap11 mutants. In the open field, Grin2a knockout mice display hyperlocomotion and an abnormal organization of naturalistic behaviors. They also displayed heightened behavioral responses to objects and auditory stimuli. Grin2a heterozygous animals mostly showed intermediate phenotypes, suggesting a dose-dependent effect of Grin2a loss. Further, Grin2a knockout mutants exhibited aberrant dopamine events, altered coupling of dopamine with locomotor features, and exaggerated stimuli-evoked dopamine responses. Notably, heterozygous animals also showed altered striatal SPN events in the open field reflecting dysregulated neural activity in both dSPNs and iSPNs. Compared to Grin2a mutants, Akap11 mutants displayed opposite phenotypes, showing reduced locomotion with a shift from high- to low-velocity movement and distinct alterations in striatal neural activity. Together, GRIN2A (SCZ risk) and AKAP11 (BD/SCZ risk) mutations induce different, often opposite, effects on striatal dopamine signaling and behavior, suggesting that these two risk genes act through distinct mechanisms.

neuroscience↗