Biology subjects

Zeman, P.

Publications and source records attributed to Zeman, P..

5 recordsLinked to original sources

bioRxiv2025

A simple, open-source restraint system for magnetic resonance imaging in awake rats

Magnetic resonance imaging (MRI) is a critical tool for translational neuroscience, offering cross-species insights into brain structure and function; however, its application in preclinical research is constrained by routine anesthesia use or sedation, which alters neural activity and limits comparisons to awake human imaging. Awake rodent functional MRI (fMRI) provides a powerful platform for investigating brain function under physiologically relevant conditions, but implementation is limited by technical challenges, particularly head motion and stress during scanning. Most restraint systems employ initial anesthesia, compromising translatability of findings, and highlighting the need for improved designs. We developed a novel restraint system optimized for awake rat fMRI. The system consists of modular 3D-printed components and can be assembled in under five minutes. It is accompanied by a protocol that includes head-post implantation followed by an 11-day habituation period post-surgical recovery. The system eliminates the need for isoflurane anesthesia, ear bars, and bite bars, reducing stress and improving animal comfort. It supports integration with behavioral paradigms such as pupil tracking and licking responses. High-resolution T2-weighted anatomical images and functional scans obtained using the system showed excellent spatial clarity and minimal motion artifacts. Quality control metrics, including head motion parameters and temporal signal-to-noise ratio, confirmed the systems stability and suitability for awake imaging. Functional connectivity analysis revealed robust positive correlations between functionally relevant regions. This system offers a scalable, reproducible, and animal-friendly solution for awake rat fMRI. While the current design limits direct cranial access for multimodal recordings, it enables high-quality, behaviorally enriched imaging without anesthesia. Significance Statement: Most rodent fMRI studies, including awake studies, rely on anesthesia, which profoundly alters brain activity and limits the interpretation of the data. This study presents a novel restraint system that enables high-quality fMRI in fully awake rats, eliminating the need for anesthesia, ear bars, and bite bars. By reducing stress and motion, this simple restraint system allows for investigation of neural activity and connectivity without confounds from sedation or anesthesia. Its open-source, modular design supports behavioral tasks and broad accessibility, making it a valuable tool for neuroscience research seeking to bridge the gap between preclinical imaging and real-world brain function.

neuroscience↗

bioRxiv2025

A non-invasive approach to awake mouse fMRI compatible with multi-modal techniques

Mouse functional magnetic resonance imaging (fMRI) studies contribute significantly to basic fundamental and translational neuroscience research. Performing fMRI in awake mice could facilitate complex tasks in the magnet and improve translational validity by avoiding anesthesia-related neural and neurovascular changes. Existing surgical approaches provide excellent motion control but are not desirable for all experiments aiming to scan awake mice. These include studies with transgenic mouse lines that are vulnerable to anesthesia or mice in longitudinal studies involving cognition. To address these needs, we propose a non-invasive restraint to scan mice in the awake state. The restraint was designed to be compatible with brain stimulation and recording approaches often combined with fMRI. It was evaluated on the basis of motion, fMRI data quality, and animal stress levels, and compared to a conventional headpost restraint. We found the proposed approach was effective at restraining mice across a broad range of weights without the need for any anesthesia for setup. The non-invasive restraint led to higher data attrition after censoring high motion volumes, but by acquiring roughly 25% more data we could obtain comparable network spatial specificity to the headpost approach. Our results demonstrate a simple open-source head restraint that can be used for awake mouse fMRI for certain cohorts, and we establish suitable acclimation and scanning protocols for use with this restraint.

neuroscience↗

bioRxiv2024

An Open Access Resource for Marmoset Neuroscientific Apparatus

The use of the common marmoset (Callithrix jacchus) for neuroscientific inquiry has grown precipitously over the past two decades. Despite windfalls of grant support from funding initiatives in North America, Europe, and Asia to model human brain diseases in the marmoset, marmoset- specific apparatus are of sparse availability from commercial vendors and thus are often developed and reside within individual laboratories. Through our collective research efforts, we have designed and vetted myriad designs for awake or anesthetized magnetic resonance imaging (MRI), positron emission tomography (PET), computed tomography (CT), as well as focused ultrasound (FUS), electrophysiology, optical imaging, surgery, and behavior in marmosets across the age- span. This resource makes these designs openly available, reducing the burden of de novo development across the marmoset field. The computer-aided-design (CAD) files are publicly available through the Marmoset Brain Connectome (MBC) resource (https://www.marmosetbrainconnectome.org/apparatus/) and include dozens of downloadable CAD assemblies, software and online calculators for marmoset neuroscience. In addition, we make available a variety of vetted touchscreen and task-based fMRI code and stimuli. Here, we highlight the online interface and the development and validation of a few yet unpublished resources: Software to automatically extract the head morphology of a marmoset from a CT and produce a 3D printable helmet for awake neuroimaging, and the design and validation of 8-channel and 14- channel receive arrays for imaging deep structures during anatomical and functional MRI.

bioengineering↗

bioRxiv2023

Layer Dependence of Monocular and Binocular Responses in Human Ocular Dominance Columns at 7T using VASO and BOLD

The neurons located in the striate cortex (V1) preferentially respond to the input from one eye or another, forming a fingerprint-like pattern of ocular dominance columns (ODCs). At this mesoscopic scale, accessible by ultra-high field fMRI, V1 is supplied/drained by a network of surface (pial) vessels that connect to descending/ascending tangential vessels that penetrate the cortex and supply/drain a capillary bed whose density is also layer dependent. In this study, we measured the layer dependence of monocular and binocular responses of ocular dominance columns in V1 at 7T using Blood Oxygenation Level Dependent (BOLD) and VAscular Space Occupancy (VASO) contrasts. Our results indicate that the microvascular blood volume changes that give rise to VASO are well confined to the site of neural activity across the layers of the cortex and between the columns. Pial veins dominate the BOLD response and mix the signal between columns. When the GRE BOLD response was examined in only the VASO specific voxels (thus eliminating the pial vein signal), the laminar profile was very similar to VASO, however, the columnar response was still blurred. Caution needs to be exercised in the interpretation of signal changes in BOLD at the mesoscale both in terms of feedforward/feedback effects and inhibitory and excitatory effects. Highlights- VASO produced laminar profiles that were consistent with the known layer-dependent neuronal response to monocular and binocular stimulations. - VASO better differentiated the response between columns belonging to the left and right eyes. - GRE BOLD signal spatial specificity was poor in both laminar and columnar directions, however, when the pial veins were suppressed, the laminar BOLD signal was very similar to the VASO signal. - Caution needs to be exercised when interpreting cognitive neuroscience BOLD studies at the mesoscale level due to the confounding effects of pial and sub-pial veins and venules.

neuroscience↗

bioRxiv2021

Simultaneous functional MRI of socially interacting marmosets

Social cognition is a dynamic process that requires the perception and integration of a complex set of idiosyncratic features between interacting conspecifics. Here we present a method for simultaneously measuring the whole-brain activation of two socially interacting marmoset monkeys using functional magnetic resonance imaging. MRI hardware (a radiofrequency coil and peripheral devices) and image-processing pipelines were developed to assess brain responses to socialization, both on an intra-brain and inter-brain level. Notably, brain-activation maps acquired during constant interaction demonstrated neuronal synchrony between marmosets in regions of the brain responsible for processing social interaction. This method enables a wide range of possibilities for studying social function and dysfunction in a non-human primate model, including using transgenic models of neuropsychiatric disorders.

neuroscience↗