Novel functional and anatomical imaging approaches for the nervous system studies

25.04.2026, Saturday, 15:15-17:00

Chair: Bartosz Pomierny & Mateusz Kucharczyk
Jagiellonian University, Kraków, Poland

Lukasiewicz Research Network – PORT Polish Center for Technology Development, Wroclaw, Poland

General focus of the symposium:

The symposium will showcase complementary imaging strategies that together enable a multi-scale view of the nervous system, from cellular activity to whole-brain organisation. The common theme is the integration of advanced optical and magnetic resonance imaging (MRI) methods with robust analysis pipelines that make these techniques reproducible and transferable between laboratories.

The first part will focus on functional imaging using genetically encoded calcium indicators such as GCaMP, combined with high-speed optical microscopy. These approaches allow monitoring of activity in defined neuronal populations with high temporal resolution and can be aligned with behavioural paradigms and disease models to dissect circuit-level mechanisms. In parallel, light-sheet microscopy, including mesoSPIM implementations, will be presented as a powerful tool for three-dimensional anatomical mapping in cleared brain and spinal cord tissue, enabling quantitative analysis of connectivity, vascular architecture and activity markers across large volumes.

The second part will highlight recent developments in MRI-based analysis frameworks for neuroscience. Particular emphasis will be placed on methods for accurate co-registration of MRI with optical imaging readouts and spatially resolved omics data. Such integration is crucial for linking macroscopic measures of structure, perfusion and function to the underlying cellular and molecular landscape.

Finally, the symposium will address automation and standardisation of image analysis across modalities. This includes the design of reusable, containerised workflows, harmonised quality control procedures and FAIR-compliant data management strategies that facilitate data sharing and meta-analyses.

Together, the contributions will provide a coherent overview of how novel functional and anatomical imaging approaches can be combined into unified experimental pipelines, and will be relevant for basic, preclinical and translational researchers aiming to implement state-of-the-art imaging in their studies of the nervous system.

15:15 Diana Cash

BRAIN Centre, King's College London, London, England

"Preclinical fingerprinting of neuroactive drugs using pharmacological fMRI"

Drug discovery in neuroscience faces major challenges due to the inaccessibility of the brain—the primary target organ. Testing novel compounds in humans is often ethically and financially unfeasible, while animal models frequently fall short in replicating the full complexity of clinical conditions. Neuroimaging offers a promising, translatable approach to bridge the "bench-to-bedside" gap, yet preclinical imaging methods often lack sufficient standardisation.

To address this, we are developing a database of neuroimaging "fingerprints" for established neuroactive drugs, which can serve as reference points for evaluating novel therapeutics. In this talk, I will outline the key methods used for pharmacological profiling in experimental rodents and highlight areas of convergence and divergence with imaging techniques used in humans. I will also present findings from our latest study, FFIND (Functional Fingerprinting in Neuroactive Drugs), in which we acquired BOLD and ASL fMRI data for several well-characterised compounds—including ketamine, MK801, psilocybin, donepezil, clozapine, and levetiracetam. This dataset provides a framework for benchmarking novel compounds and accelerating the development of more effective treatments for brain disorders.

15:38 Marija Petrinovic

King's College London, England

"Of Mice and Mechanisms: Convergent Aggression, Divergent Biology"

Aggression is a common feature of neurodevelopmental conditions, but whether it reflects shared or distinct underlying mechanisms remains unclear. We show that similar increases in aggression can arise from divergent circuit-level activity. Importantly, these differences are accompanied by selective sensitivity to pharmacological interventions. Together, these findings demonstrate that convergent behavioral phenotypes can mask fundamentally distinct biological substrates, with
important implications for targeted therapeutic strategies.

16:00 Julia Niemczycka & Mateusz W. Kucharczyk

Cancer Neurophysiology Group, Polish Centre for Technology Development, Łukasiewicz-PORT, Wrocław, Poland

Biophotonics and Electrophysiology Lab, Imaging Laboratories, Center for the Development of Therapies for Civilization and Age-Related Diseases, Jagiellonian University Medical College, Kraków, Poland

Wolfson Sensory, Pain and Regeneration Centre, King’s College London, England

"High-Throughput Optical Microscopy Approaches for Functional Imaging and 3D Reconstruction of Neural Tissue"

Dr. Kucharczyk will introduce a practical overview of high-throughput linear and non-linear fluorescence microscopy approaches enabling (A) rapid functional sampling and (B) large-scale anatomical reconstruction across the peripheral and central nervous systems. A) Functional imaging pipelines will be demonstrated across custom-built and commercial wide-field, confocal, confocal endoscopy, and two-photon microscopes, illustrating how genetically encoded calcium indicators permit in vivo monitoring of neuronal activity in both the PNS and CNS. B) High-resolution volumetric imaging strategies will be showcased using confocal, two-photon, and light-sheet modalities, including the first Polish benchtop mesoSPIM platform developed in our laboratory.

Subsequently, PhD student Julia Niemczycka will present original datasets, including whole-organ 3D reconstructions of peripheral innervation paired with molecular profiling. A case study will revisit the specificity of transgenic reporter lines, revealing the anatomy and physiology of deep-tissue peptidergic afferents. Examples will include in vivo sensory-neuron calcium imaging in health and disease using wide-field and two-photon microscopy, as well as mesoscale reconstructions and practical experience gained during the construction of the mesoSPIM light-sheet microscope.

16:15 Karolina Nowalińska & Bartosz Pomierny

BioImaging Laboratory, Center for the Development of Therapies for Civilization and Age-Related Diseases, Jagiellonian University Medical College, Kraków, Poland

"Neuroprotective Potential of Zolpidem in Ischemic Stroke: From Molecular Mechanisms to Functional Imaging"

This talk will outline the neuroprotective potential of zolpidem in ischemic stroke, integrating pharmacological findings with novel functional and anatomical imaging approaches for nervous system studies. Using a preclinical MCAO model, we demonstrated that early, low-dose zolpidem administration reduces infarct volume and improves neurological and motor outcomes. These effects are interpreted alongside analyses of GABAergic signaling, glutamate dynamics, and chloride homeostasis. Furthermore, we investigated cortical spreading depolarizations using electrophysiological recordings. Currently, we are developing a protocol to visualize CSD using functional magnetic resonance imaging, along with a setup for continuous recordings of optogenetically induced CSD. Together, these approaches highlight how combining pharmacology with cutting-edge imaging can advance our understanding of stroke pathology and recovery mechanisms.

16:30 Kornelia Kliś

Department of Neurosurgery and Neurotraumatology, Jagiellonian University Medical College, Kraków, Poland

"The Brain Beyond the Aneurysm: from morphometry and networks to treatment effects and translational bridges"

16:45 Zofia Sikorska

SANO - Centre for Computational Personalised Medicine, Kraków, Poland

"Optimizing CNNs for Detecting Low Amplitude Eye Movements from fMRI"

The fMRI signal from the eyes provides a proxy for gaze position, enabling retrospective analysis of gaze behavior and brain activity in open datasets. While prior work has successfully decoded gaze during large-scale tasks such as smooth pursuit and free viewing, detecting small-scale eye movements that are common in open-eyes resting-state (RS) paradigms remains challenging. The subtle movements during RS carry clinically relevant information but have much lower amplitudes than large-scale gaze tasks.

In this project, we aim to develop a model to detect low-amplitude eye movements from fMRI data.

We used simultaneous fMRI and eye-tracking data from 29 participants during a resting-state fixation scan. Mean gaze amplitude was ±1°, lower than large-scale tasks (±10°). We evaluated four strategies using a CNN model pretrained on large-scale gaze tasks: (1) directly applying the pretrained model to the RS dataset; (2) augmenting the original training set with RS data; (3) training a new model using only the RS dataset; and (4) transfer learning by freezing the pretrained backbone and fine-tuning on RS data using a composite loss (Smooth L1/Huber, δ=1.0; Pearson weight=0.01; learning rate=1e-4; 40 epochs) to balance robust error minimization and trend capture.

Models pretrained on large-scale tasks systematically overestimated gaze amplitudes of RS data due to the amplitude mismatch. Training from scratch on the small RS dataset failed because of limited sample size and imbalance. The proposed transfer learning approach significantly improved performance, achieving a median Pearson correlation of 0.36 ± 0.25 between predicted and true RS gaze data.

These results demonstrate that decoding small-scale spontaneous eye movements from resting-state fMRI is feasible but requires careful domain adaptation. Correlation-aware transfer learning effectively bridges amplitude differences, unlocking the potential to extract oculomotor information from existing resting-state fMRI datasets