Wide-field optical mapping of neural activity and brain haemodynamics: considerations and novel approaches

Ultrasensitive fluorescent proteins for imaging neuronal activity

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Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics

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Selective effects of acute and chronic stress on slow and alpha-theta cortical functional connectivity and reversal with subanesthetic ketamine

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Modern Microscopic Approaches to Astrocytes

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Rebound Excitation of Epileptiform Activities by Transcranial Focused Ultrasound StimulationPreprint

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Visual stimulation drives retinotopic acetylcholine release in the mouse visual cortexPreprint

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Integrated ultrasound stimulation and optical imaging of awake mice brain using a transparent ultrasound transducer cranial window

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Multispectral intraoperative imaging for the detection of the hemodynamic response to interictal epileptiform discharges

Laurence, A., Toffa, D. H., Peng, K., Robert, M., Bouthillier, A., Nguyen, D. K., & Leblond, F. (2022) · Biomedical Optics Express · doi:10.1364/boe.465699 · Cited by 4

植入式多模态神经接口前沿进展

Mingliang, 徐. X., Fangyuan, 李. L., Yueqi, 刘. L., Jinhui, 张. Z., Yazhou, 师. S., & Fei, 何. H. (2023) · Chinese Journal of Lasers · doi:10.3788/cjl221482 · Cited by 4

Quantitative Optical Imaging of Oxygen in Brain Vasculature

Rathbone, E. G., & Fu, D. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c01277 · Cited by 4

Assessment of Pain-Induced Changes in Cerebral Microcirculation by Imaging Photoplethysmography

Kamshilin, A. A., Любашина, О. А., Volynsky, M. A., Zaytsev, V. V., & Mamontov, O. V. (2019) · Lecture notes in computer science · doi:10.1007/978-3-030-17935-9_43 · Cited by 4

Functional Monitoring and Imaging in Deep Brain Structures

Yu, L., & Murari, K. (2021) · Handbook of Neuroengineering · doi:10.1007/978-981-15-2848-4_135-1 · Cited by 4

Investigating presence of motion artifacts in the oxygen saturation signal during in-vivo fiber photometry

Bisht, A., Simone, K., Peringod, G., Gordon, G. R., Bains, J. S., & Murari, K. (2022) · Neural Imaging and Sensing · doi:10.1117/12.2609877 · Cited by 4

Real-Time Closed-Loop Feedback System For Mouse Mesoscale Cortical Signal And Movement Control: CLoPyPreprint

Gupta, P. K., & Murphy, T. H. (2025) · eLife · doi:10.7554/elife.105070.1 · Cited by 4

Bridging the gap: umIT makes complex imaging data accessible to scientists of all backgrounds

de Souza, B. O. F., Samantzis, M., Albert, C., Bélanger, S., Bouchard, J., Balbi, M., & Vanni, M. P. (2025) · Neurophotonics · doi:10.1117/1.nph.12.s1.s14616 · Cited by 3

The protocol for mesoscopic wide-field optical imaging in mice: from zero to hero

Kislukhina, E. N., Lizunova, N. V., Surin, A. M., & Валериевна, Б. З. (2025) · Biology Methods and Protocols · doi:10.1093/biomethods/bpaf090 · Cited by 3

Perinatal stroke: modelling and the potential of neurovisualization

Lizunova, N. V., Kislukhina, E. N., & Surin, A. M. (2022) · Russian Pediatric Journal · doi:10.46563/1560-9561-2022-25-2-128-138 · Cited by 3

Type-I nNOS neurons orchestrate cortical neural activity and vasomotion

Turner, K., Brockway, D. F., Hossain, M. S., Griffith, K. R., Greenawalt, D. I., Zhang, Q., Gheres, K. W., Crowley, N. A., & Drew, P. J. (2025) · eLife · doi:10.7554/elife.105649.3 · Cited by 4

Characterization of iGABASnFR2 for in vivo mesoscale imaging of intracortical GABA dynamics

Rezaei, E., Tohidi, S., Nazari, M., & Abadchi, J. K. (2025) · Neurophotonics · doi:10.1117/1.nph.12.3.035006 · Cited by 4

Cortex-wide characterization of decision-making neural dynamics during spatial navigation

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Red-shifted GRAB acetylcholine sensors for multiplex imaging in vivo

Xie, S., Miao, X., Li, G., Zheng, Y. R., Li, M., Ji, E., Wang, J., Li, S., Cai, R., Geng, L., et al. (2026) · Nature Neuroscience · doi:10.1038/s41593-026-02325-w · Cited by 4

Monitoring stimulus‐evoked hemodynamic response during deep brain stimulation with single fiber spectroscopy

Yu, L., Noor, M. S., Kiss, Z. H. T., & Murari, K. (2022) · Journal of Biophotonics · doi:10.1002/jbio.202200076 · Cited by 3

Mesoscale calcium imaging in vivo: evolution and contribution to developmental neuroscience

Guillamón-Vivancos, T., Vandael, D., Torres, D., López‐Bendito, G., & Martini, F. J. (2023) · Frontiers in Neuroscience · doi:10.3389/fnins.2023.1210199 · Cited by 3

Glutamate and ischemia-induced changes in ion homeostasis in the neuronal culture and cerebral cortex of mice expressing Ca2+-sensor GCаMP6f

Kislukhina, E. N., Lizunova, N. V., Lisinа, O., Шарипов, Р. Р., Krasilnikova, I. A., Валериевна, Б. З., Pinelis, V. G., & Surin, A. M. (2023) · Zhurnal «Patologicheskaia fiziologiia i eksperimental`naia terapiia» · doi:10.25557/0031-2991.2023.01.5-20 · Cited by 3

Mesoscopic cortical network reorganization during recovery of optic nerve injury in GCaMP6s mice

Groleau, M., Nazari-Ahangarkolaee, M., Vanni, M. P., Higgins, J., Bédard, A.-S. V., Sabel, B. A., Mohajerani, M. H., & Vaucher, E. (2020) · Scientific Reports · doi:10.1038/s41598-020-78491-z · Cited by 3

Penalized matrix decomposition for denoising, compression, and improved demixing of functional imaging dataPreprint

Buchanan, E. K., Kinsella, I., Zhou, D. X., Zhu, R., Zhou, P., Gerhard, F., Ferrante, J., Ma, Y., Kim, S. H., Shaik, M. A., et al. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1807.06203 · Cited by 3

Multimodal dataset linking wide‐field calcium imaging to behavior changes in operant lever‐pull task in mice

Kondo, M., Sehara, K., Harukuni, R., Aoki, R., Sugimoto, S., Tanaka, Y. R., Matsuzaki, M., & Nakae, K. (2025) · Scientific Data · doi:10.1038/s41597-025-05482-y · Cited by 4

Optimized Fluorescent pH-Sensitive Dextran Conjugates Enable Ratiometric Measurement of Cerebral Blood pH In Vivo and In Situ

Walter, S., Tournissac, M., Chaigneau, E. M., Charpak, S., & Collot, M. (2025) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.5c08439 · Cited by 2

Ultrafast venous and sagittal sinus constrictions in the brain driven by abdominal pressure

Zhang, Q., Garborg, C. S., Frank, N., Salehi, F., Turner, K. L., & Drew, P. J. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2604172123 · Cited by 3

Concurrent intrinsic optical imaging and fMRI at ultra‐high field using magnetic field proof optical components

Bernard, R., Salzmann, M. F. V., Scheffler, K., & Pohmann, R. (2023) · NMR in Biomedicine · doi:10.1002/nbm.4909 · Cited by 2

Audiovisualization of real-time neuroimaging data

Thibodeaux, D. N., Shaik, M. A., Kim, S. H., Voleti, V., Zhao, H., Benezra, S. E., Nwokeabia, C., & Hillman, E. M. C. (2024) · PLoS ONE · doi:10.1371/journal.pone.0297435 · Cited by 2

Continuous Auditory Feedback Promotes Fine Motor Skill Learning in Mice

Xiao, D., & Balbi, M. (2025) · eNeuro · doi:10.1523/eneuro.0008-25.2025 · Cited by 3

Contributions of synaptic glutamate versus neuronal spiking activity to cerebral vascular responses in awake mice

Peretin, J. M., Cover, C. G., & Vazquez, A. L. (2025) · Journal of Cerebral Blood Flow & Metabolism · doi:10.1177/0271678x251338407 · Cited by 2

Mapping of neurovascular and neurometabolic couplings by multimodal optical imaging

Hermán, P., Sanggaard, S., James, S., Akif, A., Mishra, S. K., Sanganahalli, B. G., Verhagen, J. V., Blumenfeld, H., & Hyder, F. (2025) · Cerebral Cortex · doi:10.1093/cercor/bhaf165 · Cited by 2

A miniaturized intrinsic optical sensing system (MiniIOS) for hemodynamic monitoring in freely-behaving rodents

Yu, L., & Murari, K. (2019) · Neural Imaging and Sensing · doi:10.1117/12.2507110 · Cited by 2

Functional Monitoring and Imaging in Deep Brain Structures

Yu, L., & Murari, K. (2023) · Handbook of Neuroengineering · doi:10.1007/978-981-16-5540-1_135 · Cited by 2

Ketamine-induced 1-Hz oscillation of spontaneous neural activity is not directly visible in the hemodynamics

Li, R., Ohki, K., & Matsui, T. (2023) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2023.08.034 · Cited by 2

System for simultaneous measurement of fluorescence and hemodynamics (SSMFH) from deep brain regions of freely moving rodents

Bisht, A., Peringod, G., Gordon, G. R., Bains, J. S., & Murari, K. (2024) · Neural Imaging and Sensing · doi:10.1117/12.3002776 · Cited by 2

Isolated correlates of somatosensory perception in the mouse posterior cortexPreprint

Sokoletsky, M., Ungarish, D., Katz, Y., & Lampl, I. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.16.498499 · Cited by 2

Antipsychotic drugs selectively decorrelate long-range interactions in deep cortical layersPreprint

Heindorf, M., & Keller, G. B. (2023) · doi:10.7554/elife.86805.1 · Cited by 2

Antipsychotic drugs selectively decorrelate long-range interactions in deep cortical layersPreprint

Heindorf, M., & Keller, G. B. (2024) · eLife · doi:10.7554/elife.86805.3 · Cited by 2

Multimodal alignments of in vivo imaging and spatial biology datasets at cellular resolutionPreprint

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Energy paradox in REM sleep: balancing supply and consumption in brain metabolism

Takahashi, Y., Ikoma, Y., & Matsui, K. (2026) · Communications Biology · doi:10.1038/s42003-026-10646-6 · Cited by 1

Development of optical methods for real-time whole-brain functional imaging of zebrafish neuronal activity

Turrini, L. (2020) · Premio Tesi dottorato/Premio Tesi di dottorato · doi:10.36253/978-88-5518-070-2 · Cited by 1

Low-cost reversible tandem lens mesoscope for brain imaging in rodents

Jose, A., Cheung, P. Y., Laouby, Z., Vanholsbeeck, F., & Cheyne, J. E. (2024) · Neurophotonics · doi:10.1117/1.nph.11.1.014306 · Cited by 1

Predicting animal behavior from neuronal miniscope data: a deep learning approach

Das, S., Senarathna, J., Ouyang, E., Banerjee, A., & Pathak, A. P. (2024) · SPIE Medical Imaging: Image Processing · doi:10.1117/12.3006089 · Cited by 1

Evaluation of calibrated and uncalibrated optical imaging approaches for relative cerebral oxygen metabolism measurements in awake mice

Toader, A. E., Fukuda, M., & Vazquez, A. L. (2024) · Physiological Measurement · doi:10.1088/1361-6579/ad3a2d · Cited by 1

Refining hemodynamic correction in in vivo wide-field fluorescent imaging through linear regression analysis

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Mesoscopic Imaging of Neurotransmitters and Neuromodulators with Genetically Encoded Sensors

Deng, F., Feng, J., Xie, H., & Li, Y. (2024) · Neuromethods · doi:10.1007/978-1-0716-4120-0_1 · Cited by 1

High-quality simultaneous bright-field and dark-field imaging based on the light-field matrix model

Liu, K., Wu, J., Cao, J., Zhuo, R., Chen, X., Zhou, Q., Wang, P., & Shi, G. (2025) · Applied Physics Letters · doi:10.1063/5.0253792 · Cited by 1

Interhemispheric resting-state functional connectivity correlates with spontaneous neural interactions

Moon, H. S., Vo, T. T., Im, G. H., Hong, S., & Kim, S. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2505294122 · Cited by 1

Chronic alteration of Ca2+ and hemodynamic signals induced by intracortical microstimulation in the visual cortex of awake mice

Suematsu, N., Vazquez, A. L., & Kozai, T. D. Y. (2026) · Biomaterials · doi:10.1016/j.biomaterials.2026.124276 · Cited by 2

Disassociating cerebral vasomotion from low frequency spontaneous neurovascular coupling

Wang, R., Patel, P., Boorman, L. W., Okun, M., Howarth, C., & Berwick, J. (2025) · Scientific Reports · doi:10.1038/s41598-025-27705-3 · Cited by 1

Simultaneous mesoscopic imaging of neural activity and hemodynamics reveals anesthetic modulation of neurovascular responses

Wen, R., Qin, W., Li, B., Li, T., & Xi, L. (2026) · Photoacoustics · doi:10.1016/j.pacs.2026.100874 · Cited by 1

Attention-based CNN-BiLSTM for sleep state classification of spatiotemporal wide-field calcium imaging data

Zhang, X., Landsness, E. C., Culver, J. P., Lee, J., & Anastasio, M. A. (2023) · Neural Imaging and Sensing · doi:10.1117/12.2649375 · Cited by 1

TinyIOMS: A Wireless Miniaturised System for Monitoring Hemodynamics from Surface Brain Regions

Bisht, A., Yu, L., Cheng, N., & Murari, K. (2023) · IEEE Biomedical Circuits and Systems Conference (BioCAS) · doi:10.1109/biocas58349.2023.10388820 · Cited by 1

Spatial nonstationarity of image noise in widefield optical imaging and its effects on cluster-based inference for resting-state functional connectivity

White, B. R., Adepoju, T. E., Fisher, H. B., Shinohara, R. T., & Vandekar, S. (2024) · Journal of Neuroscience Methods · doi:10.1016/j.jneumeth.2024.110076 · Cited by 2

BLEscope: A Bluetooth Low Energy (BLE) Microscope for Wireless Multicontrast Functional Imaging

Das, S., Senarathna, J., Ren, Y., Dinh, V., Ying, M., Etienne-Cummings, R., & Pathak, A. P. (2024) · IEEE Transactions on Biomedical Engineering · doi:10.1109/tbme.2024.3467221 · Cited by 1

Analysis of Mesoscope Imaging Data

Zhang, Y., & Saxena, S. (2024) · Neuromethods · doi:10.1007/978-1-0716-4120-0_2 · Cited by 1

Mesoscopic Mapping of Stimulus-Selective Response Plasticity in the Visual Pathways Modulated by the Cholinergic System

Laliberté, G., Othman, R., & Vaucher, E. (2020) · Frontiers in Neural Circuits · doi:10.3389/fncir.2020.00038 · Cited by 1

Multimodal Detection for Cryptogenic Epileptic Seizures Based on Combined Micro Sensors

Shen, Z., Jiao, Y., Xu, Y., Shi, W., Yang, C., Li, D., Ma, H., Shao, W., Li, Z., & Cui, Y. (2020) · BioMed Research International · doi:10.1155/2020/5734932 · Cited by 1

Automated classification of signal sources in mesoscale calcium imagingPreprint

Mullen, B. R., Weiser, S. C., Ascencio, D., & Ackman, J. B. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.23.432573 · Cited by 1

Variability in sampling of cortex-wide neural dynamics explains individual differences in functional connectivity and behavioral phenotypePreprint

MacDowell, C. J., Briones, B. A., Lenzi, M. J., Gustison, M. L., & Buschman, T. J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.24.477572 · Cited by 1

Wide-field Calcium Imaging Reveals Widespread Changes in Cortical Connectivity Following Repetitive, Mild Traumatic Brain Injury in the MousePreprint

Cramer, S. W., Haley, S. P., Popa, L. S., Carter, R. E., Scott, E. P., Flaherty, E. B., Dominguez, J., Aronson, J. D., Sabal, L., Surinach, D. A., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.22.481459 · Cited by 1

Bidirectional alterations in brain temperature profoundly modulate spatiotemporal neurovascular responses in-vivo: Implications for theragnosticsPreprint

Boorman, L. W., Harris, S., Shabir, O., Lee, L., Eyre, B., Howarth, C., & Berwick, J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.14.488315 · Cited by 1

Antipsychotic drugs selectively decorrelate long-range interactions in deep cortical layersPreprint

Heindorf, M., & Keller, G. B. (2023) · doi:10.7554/elife.86805.2 · Cited by 1

Longitudinal Awake Imaging of Deep Mouse Brain Microvasculature with Super-resolution Ultrasound Localization MicroscopyPreprint

Wang, Y., Lowerison, M. R., You, Q., Lin, B., Llano, D. A., & Song, P. (2024) · eLife · doi:10.7554/elife.95168.1 · Cited by 1

Reactive Pericytes Lead to Microvascular Dysfunction and Cortical Neurodegeneration During Experimental Autoimmune EncephalomyelitisPreprint

Yousefi, M., Özkan, A., Özmen, K. K., Uysallı, Y., Mamipour, M., Akkaya, N., Amandi, A.-R. D., Atbaşi, A., Heidarzadeh, M., Erdener, Ş. E., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.17.638582 · Cited by 1

Quantification of the effect of hemodynamic occlusion in two-photon imagingPreprint

Yogesh, B., Heindorf, M., Jordan, R., & Keller, G. B. (2025) · eLife · doi:10.7554/elife.104914.2 · Cited by 1

Type-I nNOS neurons orchestrate cortical neural activity and vasomotionPreprint

Turner, K. L., Brockway, D. F., Hossain, M. S., Griffith, K. R., Greenawalt, D. I., Zhang, Q., Gheres, K. W., Crowley, N. A., & Drew, P. J. (2025) · eLife · doi:10.7554/elife.105649 · Cited by 1

Type-I nNOS neurons orchestrate cortical neural activity and vasomotionPreprint

Turner, K. L., Brockway, D. F., Hossain, M. S., Griffith, K. R., Greenawalt, D. I., Zhang, Q., Gheres, K. W., Crowley, N. A., & Drew, P. J. (2025) · eLife · doi:10.7554/elife.105649.1 · Cited by 2

Mesoscopic SCAPE Microscope with a Rescanned, Super-oblique Illumination PlanePreprint

Cao, Z., Jiapeng, 朱. Z., Zhang, C. H., Wang, Q., Huang, Y., Liu, W., Shen, B., Chai, Y., Zhong, Z., He, L., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.25.650616 · Cited by 1

Cortical GABAergic inhibition dynamics around hippocampal sharp-wave ripplesPreprint

Rezaei, E., Tohidi, S., Nazari, M., McNaughton, B. L., & Mohajerani, M. H. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.17.670701 · Cited by 1

Longitudinal Awake Imaging of Mouse Deep Brain Microvasculature with Super-resolution Ultrasound Localization MicroscopyPreprint

Wang, Y., Lowerison, M. R., Huang, Z., You, Q., Lin, B., Llano, D. A., & Song, P. (2025) · eLife · doi:10.7554/elife.95168.3 · Cited by 1

Increasing sensitivity and accuracy of brain-wide quantitative studies in light-sheet microscopyPreprint

Müllenbroich, M. C., Silvestri, L., Turrini, L., Alterini, T., Giovanna, A. P. D., Costantini, I., Gheisari, A., Vanzi, F., Sacconi, L., & Pavone, F. S. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/230540

Computational methods for predicting behavior from neuroimaging data

Zhu, L. (2018) · doi:10.7282/t3-h6r0-fa15

A Mini Microscope Implanted in Brain of Freely Moving, Unanesthetized Mice Permits Weeks of Imaging

Hurley, D. (2019) · Neurology Today · doi:10.1097/01.nt.0000559873.15103.25

Intraoperative Monitoring of Cerebral Hemodynamics by Camera-Based Photoplethysmography

Kamshilin, A. A., Mamontov, O. V., & Shcherbinin, A. V. (2019) · Imaging and Applied Optics · doi:10.1364/isa.2019.ith3b.3

DEVELOPEMENT OF WIDEFIELD MULTI-CONTRAST OPTICAL METHODS FOR IN VIVO MICROVASCULAR SCALE IMAGING

Senarathna, D. M. M. J. (2017)

Dual brain cortical calcium imaging reveals social interaction-specific correlated activity in micePreprint

Michelson, N. J., Bolaños, F., Bolaños, L. A., Balbi, M., LeDue, J. M., & Murphy, T. H. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.20383/101.0303 · Cited by 4

Multi-parametric characterization of brain-wide hemodynamic and calcium responses to sensory stimulation in micePreprint

Chen, Z., Zhou, Q., Deán‐Ben, X. L., Gezginer, I., Ni, R., Reiss, M., Shoham, S., & Razansky, D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.08.467725

Poster Viewing Sessions PA00-A01 to PA00-A49

de la Colina, A. N., Badji, A., Sabra, D., Karakuzu, A., Joubert, S., Bherer, L., Lamarre-Cliche, M., Gauthier, C. J., Cohen‐Adad, J., & Girouard, H. (2019) · Journal of Cerebral Blood Flow & Metabolism · doi:10.1177/0271678x19851017

Spatial and Temporal Comparisons of Calcium Channel and Intrinsic Signal Imaging During in Vivo Cortical Spreading Depolarizations in Healthy and Hypoxic Brains

LaSarge, C. L., McCoy, C., Namboodiri, D. V., Hartings, J. A., Danzer, S. C., Batie, M. R., & Skoch, J. M. (2022) · Neurocritical Care · doi:10.1007/s12028-022-01660-7

Reviewer #3 (Public Review): Antipsychotic drugs selectively decorrelate long-range interactions in deep cortical layers

Matthias, H., & Keller Georg, B. (2023) · doi:10.7554/elife.86805.1.sa0

eLife Assessment: Antipsychotic drugs selectively decorrelate long-range interactions in deep cortical layers

Kok, P. (2023) · doi:10.7554/elife.86805.1.sa3

Reviewer #1 (Public Review): Antipsychotic drugs selectively decorrelate long-range interactions in deep cortical layers

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Reviewer #2 (Public Review): Antipsychotic drugs selectively decorrelate long-range interactions in deep cortical layers

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