Software for controlling advanced multi-photon and laser scanning microscopes
MBF Bioscience > ScanImage®

Product Overview

Don’t let the microscope control you! ScanImage is a software package for controlling multiphoton and laser scanning microscopes. It enables advanced techniques such as time multiplexed acquisition and single photon counting. ScanImage uses the powerful vDAQ hardware for controlling all aspects of the microscope. ScanImage runs on custom-built microscopes and on commercial microscopes from Scientifica, Sutter Instruments, Prospective Instruments, and Thorlabs.

product image vidrio
Play Video

Key Benefits

ScanImage software is the professional’s tool of choice for controlling multi-photon laser scanning microscopes. Enabling cutting-edge microscopy solutions for more than 2 decade, it has been cited in more than 900 research papers. ScanImage can be used to control 2-photon and 3-photon microscopes and laser scanning confocals using techniques such as, linear scanning, resonant scanning, photostimulation, holography, and has advanced techniques such as time correlated single photon counting and time multiplexed acquisition. Using MATLAB based accessible source code, it can be customized and adapted by the microscope user to enable new workflows. The rich scripting API allows users to fully automate experiment workflows. ScanImage is supported by a team of engineers who work with leading microscopy experts and commercial entities to ensure the latest techniques and hardware are incorporated in its regular software updates.

Recommended Hardware Requirements
64-bit Windows 10 or 11 operating system
16 GB memory
vDAQ for microscope control

Case Study: New York University

Scientists use ScanImage to monitor dopamine-induced brain activity in a model of Parkinson’s disease
>>Learn More

Case Study: Max Planck Florida Institute for Neuroscience

In Vivo Two-Photon Synaptic Imaging with ScanImage — New Findings Challenge the Hebbian Theory of Plasticity
>>Learn More

Case Study

ScanImage Enables Cutting Edge Visual Cortex Research
>> Learn More

Eleftheriou, A., L. Ravotto, et al. (2022). "Simultaneous dynamic glucose-enhanced (DGE) MRI and fiber photometry measurements of glucose in the healthy mouse brain." NeuroImage: 119762.

Lin, J., Z. Cheng, et al. (2022). "Optical gearbox enabled versatile multiscale high-throughput multiphoton functional imaging." Nature Communications 13(1): 6564.

Wang, H. C., A. M. LeMessurier, et al. (2022). "Tuning instability of non-columnar neurons in the salt-and-pepper whisker map in somatosensory cortex." Nature Communications 13(1): 6611.

Massengill, C. I., L. Bayless-Edwards, et al. (2022). "Sensitive genetically encoded sensors for population and subcellular imaging of cAMP in vivo." Nature Methods.

Svara, F., D. Förster, et al. (2022). "Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain." Nature Methods.

Uguz, I. and K. L. Shepard (2022). "Spatially controlled, bipolar, cortical stimulation with high-capacitance, mechanically flexible subdural surface microelectrode arrays." Sci Adv 8(42): 19. DOI: 10.1126/sciadv.abq6354

Matteucci, G., M. Guyoton, et al. (2022). "Cortical sensory processing across motivational states during goal-directed behavior." Neuron.

Li, X., Y. Li, et al. (2022). "Real-time denoising enables high-sensitivity fluorescence time-lapse imaging beyond the shot-noise limit." Nature Biotechnology.

Franke, K., K. F. Willeke, et al. (2022). "State-dependent pupil dilation rapidly shifts visual feature selectivity." Nature 610(7930): 128-134.

Polesel, M., M. Kaminska, et al. (2022). "Spatiotemporal organisation of protein processing in the kidney." Nature Communications 13(1): 5732.

Hagai, H.-G., G. Lior, et al. (2022). "Versatile software and hardware combo enabling photon counting acquisition and real-time display for multiplexing, 2D and continuous 3D two-photon imaging applications." Neurophotonics 9(3): 031920.

Kanamori, T. and T. D. Mrsic-Flogel (2022). "Independent response modulation of visual cortical neurons by attentional and behavioral states." Neuron.

Rabinovich, R. J., D. D. Kato, et al. (2022). "Learning enhances encoding of time and temporal surprise in mouse primary sensory cortex." Nature Communications 13(1): 5504.

Li, M., H. Zhou, et al. (2022). "Activation of VIP interneurons in the prefrontal cortex ameliorates neuropathic pain aversiveness." Cell Reports 40(11): 111333.

Au - Yuan, Y. and F. Au - Lu (2022). "A Flexible Chamber for Time-Lapse Live-Cell Imaging with Stimulated Raman Scattering Microscopy." JoVE(186): e64449. doi:10.3791/64449 (2022).

DePiero, V. J. and B. G. Borghuis (2022). "Phase advancing is a common property of multiple neuron classes in the mouse retina." eneuro: ENEURO.0270-0222.2022.

Pettit, N. L., E.-L. Yap, et al. (2022). "Fos ensembles encode and shape stable spatial maps in the hippocampus." Nature.

Spampinato, G. L. B., E. Ronzitti, et al. (2022). "All-optical inter-layers functional connectivity investigation in the mouse retina." Cell Reports Methods 2(8): 100268.

Liu, Z., X. Lu, et al. (2022). "Sustained deep-tissue voltage recording using a fast indicator evolved for two-photon microscopy." Cell.

Aggarwal, A., R. Liu, et al. (2022). "Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission." bioRxiv: 2022.2002.2013.480251.

Voitov, I. and T. D. Mrsic-Flogel (2022). "Cortical feedback loops bind distributed representations of working memory." Nature.

Pettit, N. L., X. C. Yuan, et al. (2022). "Hippocampal place codes are gated by behavioral engagement." Nature Neuroscience.

Hattori, R. and T. Komiyama (2022). "Longitudinal two-photon calcium imaging with ultra-large cranial window for head-fixed mice." STAR Protocols 3(2): 101343.

Georgiou, C., V. Kehayas, et al. (2022). "A subpopulation of cortical VIP-expressing interneurons with highly dynamic spines." Communications Biology 5(1): 352.

Summers, M. T. and M. B. Feller (2022). "Distinct inhibitory pathways control velocity and directional tuning in the mouse retina." Current Biology.

Suzuki, N., M. L. S. Tantirigama, et al. (2022). "Fast and slow feedforward inhibitory circuits for cortical odor processing." eLife 11: e73406. DOI: 10.7554/eLife.73406

Hösli, L., M. Zuend, et al. (2022). "Direct vascular contact is a hallmark of cerebral astrocytes." Cell Reports 39(1): 110599.

Fearey, B. C., L. Binkle, et al. (2022). "A glibenclamide-sensitive TRPM4-mediated component of CA1 excitatory postsynaptic potentials appears in experimental autoimmune encephalomyelitis." Scientific Reports 12(1): 6000.

Ammer, G., R. M. Vieira, et al. (2022). "Anatomical distribution and functional roles of electrical synapses in Drosophila." Current Biology.

Formozov, A., M. Chini, et al. (2022). "Calcium Imaging and Electrophysiology of hippocampal Activity under Anesthesia and natural Sleep in Mice." Scientific Data 9(1): 113.

Horgan, C. C., M. Jensen, et al. (2022). "Hybrid confocal Raman endomicroscopy for morpho-chemical tissue characterization." Biomedical Optics Express 13(4): 2278-2285.

Zong, W., H. A. Obenhaus, et al. "Large-scale two-photon calcium imaging in freely moving mice." Cell. 

Chen, K., Q. Hu, et al. (2022). "Inhibition of unfolded protein response prevents post-anesthesia neuronal hyperactivity and synapse loss in aged mice." Aging Cell n/a(n/a): e13592. 10.1111/acel.13592

Livezey, J. A., P. S. Sachdeva, et al. (2022). "Not optimal, just noisy: the geometry of correlated variability leads to highly suboptimal sensory coding." bioRxiv: 2022.2003.2008.483488.

Park, A., V. Croset, et al. (2022). "Gliotransmission of D-serine promotes thirst-directed behaviors in <em>Drosophila</em&gt." bioRxiv: 2022.2003.2007.483255.

Weiler, S., D. Guggiana Nilo, et al. (2022). "Orientation and direction tuning align with dendritic morphology and spatial connectivity in mouse visual cortex." Current Biology.

Hösli, L., N. Binini, et al. (2022). "Decoupling astrocytes in adult mice impairs synaptic plasticity and spatial learning." Cell Reports 38(10): 110484.

Yildirim, M., C. Delepine, et al. (2022). "Label-free three-photon imaging of intact human cerebral organoids: tracking early events in brain development and deficits in Rett Syndrome." bioRxiv: 2022.2002.2028.482282.

Gellner, A.-K., A. Sitter, et al. (2022). "Stress vulnerability shapes disruption of motor cortical neuroplasticity." Translational Psychiatry 12(1): 91.

Handley, E. E., L. A. Reale, et al. (2022). "Estrogen Enhances Dendrite Spine Function and Recovers Deficits in Neuroplasticity in the prpTDP-43A315T Mouse Model of Amyotrophic Lateral Sclerosis." Molecular Neurobiology.

Heintz, T. G., A. J. Hinojosa, et al. (2022). "Opposite forms of adaptation in mouse visual cortex are controlled by distinct inhibitory microcircuits." Nature Communications 13(1): 1031. 10.1038/s41467-022-28635-8

Turner, N. L., T. Macrina, et al. (2022). "Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity." Cell.

Murphy-Baum, B. L. and G. B. Awatramani (2022). "Parallel processing in active dendrites during periods of intense spiking activity." Cell Reports 38(8): 110412.

Xie, Y., A. T. Kuan, et al. (2022). "Astrocyte-neuron crosstalk through Hedgehog signaling mediates cortical synapse development." Cell Reports 38(8): 110416.

Ahn, S. J., N. E. Ruiz-Uribe, et al. (2020). "Label-free assessment of hemodynamics in individual cortical brain vessels using third harmonic generation microscopy." Biomedical Optics Express 11(5): 2665-2678. 10.1364/boe.385848

Arkhipov, A., N. W. Gouwens, et al. (2018). "Visual physiology of the layer 4 cortical circuit in silico." PLOS Computational Biology 14(11): e1006535. 10.1371/journal.pcbi.1006535

Baker, C. A., C. McKellar, et al. (2021). "Neural Network Organization for Courtship Song Feature Detection in <em>Drosophila</em&gt." bioRxiv: 2020.2010.2008.332148. 10.1101/2020.10.08.332148

Bakker, G.-J., S. Weischer, et al. (2022). "Intravital deep-tumor single-beam 3-photon, 4-photon, and harmonic microscopy." eLife 11: e63776. 10.7554/eLife.63776

Bale, M. R., M. Bitzidou, et al. (2020). "Learning a tactile sequence induces selectivity to action decisions and outcomes in the mouse somatosensory cortex." bioRxiv: 2020.2004.2017.037143. 10.1101/2020.04.17.037143

Barz, C. S., P. M. Garderes, et al. (2021). "Functional and Structural Properties of Highly Responsive Somatosensory Neurons in Mouse Barrel Cortex." Cerebral Cortex 31(10): 4533-4553. 10.1093/cercor/bhab104

Bounds, H. A., M. Sadahiro, et al. (2021). "Multifunctional Cre-dependent transgenic mice for high-precision all-optical interrogation of neural circuits." bioRxiv: 2021.2010.2005.463223. 10.1101/2021.10.05.463223

Deverett, B., S. A. Koay, et al. (2018). "A cerebellar role in evidence-guided decision-making." bioRxiv: 343095. 10.1101/343095

Engelhard, B., J. Finkelstein, et al. (2018). "Specialized and spatially organized coding of sensory, motor, and cognitive variables in midbrain dopamine neurons." bioRxiv: 456194. 10.1101/456194

Gaffield, M. A. and J. M. Christie (2021). "The cerebellum encodes and influences the initiation and termination of discontinuous movements." bioRxiv: 2021.2006.2024.449622. 10.1101/2021.06.24.449622

Hong, S. Z., L. Mesik, et al. (2021). "Norepinephrine Potentiates and Serotonin Depresses Visual Cortical Responses by Transforming Eligibility Traces." bioRxiv: 2021.2006.2022.449441. 10.1101/2021.06.22.449441

Klapoetke, N. C., A. Nern, et al. (2017). "Ultra-selective looming detection from radial motion opponency." Nature 551(7679): 237-241. 10.1038/nature24626

Lyall, E. H., D. P. Mossing, et al. (2020). "Synthesis of higher order feature codes through stimulus-specific supra-linear summation." bioRxiv: 2020.2006.2024.169359. 10.1101/2020.06.24.169359

Nagai, J., A. Bellafard, et al. (2021). "Specific and behaviorally consequential astrocyte Gq GPCR signaling attenuation in vivo with iβARK." Neuron 109(14): 2256-2274.e2259.

Orlova, N., F. Najafi, et al. (2021). "Multiplane Mesoscope reveals distinct cortical interactions following expectation violations." bioRxiv: 2020.2010.2006.328294. 10.1101/2020.10.06.328294

Pichler, P. and L. Lagnado (2018). "Hair cells with heterogeneous transfer characteristics encode mechanical stimuli in the lateral line of zebrafish." bioRxiv: 261669. 10.1101/261669

Rübel, O., A. Tritt, et al. (2021). "The Neurodata Without Borders ecosystem for neurophysiological data science." bioRxiv: 2021.2003.2013.435173. 10.1101/2021.03.13.435173

Sharma, A., A. Goring, et al. (2021). "Multiscale molecular profiling of pathological bone resolves sexually dimorphic control of extracellular matrix composition." Disease Models & Mechanisms 14(3). 10.1242/dmm.048116

Shin, J. (2021). "Perirhinal feedback input controls neocortical memory formation via layer 1." 

Stein, I. S., T. C. Hill, et al. (2019). Two-Photon Glutamate Uncaging to Study Structural and Functional Plasticity of Dendritic Spines. Multiphoton Microscopy. E. Hartveit. New York, NY, Springer New York: 65-85. 10.1007/978-1-4939-9702-2_4

Takemura, S.-y., Y. Aso, et al. (2017). "A connectome of a learning and memory center in the adult Drosophila brain." eLife 6: e26975. 10.7554/eLife.26975

Vierock, J., S. Rodriguez-Rozada, et al. (2021). "BiPOLES is an optogenetic tool developed for bidirectional dual-color control of neurons." Nature Communications 12(1): 4527. 10.1038/s41467-021-24759-5

Westermann, L. M., L. Fleischhauer, et al. (2020). "Imbalanced cellular metabolism compromises cartilage homeostasis and joint function in a mouse model of mucolipidosis type III gamma." Disease Models & Mechanisms 13(11). 10.1242/dmm.046425

Zhou, P., J. Reimer, et al. (2020). "EASE: EM-Assisted Source Extraction from calcium imaging data." bioRxiv: 2020.2003.2025.007468. 10.1101/2020.03.25.007468

Aggarwal, A., R. Liu, et al. (2022). "Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission." bioRxiv: 2022.2002.2013.480251.

Bakker, G.-J., S. Weischer, et al. (2022). "Intravital deep-tumor single-beam 3-photon, 4-photon, and harmonic microscopy." eLife 11: e63776. 10.7554/eLife.63776

Barbara, R., M. N. Kantharaju, et al. (2022). "PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish." bioRxiv: 2022.2002.2013.480249.

Adoff, M. D., J. R. Climer, et al. (2021). "The functional organization of excitatory synaptic input to place cells." Nature Communications 12(1): 3558. 10.1038/s41467-021-23829-y

Afrashteh, N., S. Inayat, et al. (2021). "Spatiotemporal structure of sensory-evoked and spontaneous activity revealed by mesoscale imaging in anesthetized and awake mice." Cell Reports 37(10): 110081.

Au - Jongbloets, B. C., L. Au - Ma, et al. (2019). "Visualizing Protein Kinase A Activity In Head-fixed Behaving Mice Using In Vivo Two-photon Fluorescence Lifetime Imaging Microscopy." JoVE(148): e59526. doi:10.3791/59526

Au - Wang, Z., S. Au - McCracken, et al. (2021). "Transpupillary Two-photon In vivo Imaging of the Mouse Retina." JoVE(168): e61970. doi:10.3791/61970

Brown, J., I. Antón Oldenburg, et al. (2020). "Spatial integration during active tactile sensation drives elementary shape perception." bioRxiv: 2020.2003.2016.994145. 10.1101/2020.03.16.994145

Chen, C., S. Agrawal, et al. (2021). "Functional architecture of neural circuits for leg proprioception in Drosophila." Current Biology 31(23): 5163-5175.e5167.

Cheng, Z., Y. Han, et al. (2021). "Probing neuronal functions with precise and targeted laser ablation in the living cortex." Optica 8(12): 1559-1572. 10.1364/optica.433562

Churgin, M. A., D. Lavrentovich, et al. (2021). "Neural correlates of individual odor preference in <em>Drosophila</em&gt." bioRxiv: 2021.2012.2024.474127. 10.1101/2021.12.24.474127

Collins, L., L. Boddington, et al. (2021). "Vagus nerve stimulation induces widespread cortical and behavioral activation." Current Biology 31(10): 2088-2098.e2083.

Deverett, B., S. A. Koay, et al. (2018). "Cerebellar involvement in an evidence-accumulation decision-making task." eLife 7: e36781. 10.7554/eLife.36781

Doron, G., N. Shin Jiyun, et al. (2020). "Perirhinal input to neocortical layer 1 controls learning." Science 370(6523): eaaz3136. 10.1126/science.aaz3136

Dürst, C. D., J. S. Wiegert, et al. (2019). "High-speed imaging of glutamate release with genetically encoded sensors." Nature Protocols 14(5): 1401-1424. 10.1038/s41596-019-0143-9

Engelhard, B., J. Finkelstein, et al. (2019). "Specialized coding of sensory, motor and cognitive variables in VTA dopamine neurons." Nature 570(7762): 509-513. 10.1038/s41586-019-1261-9

Esmaeili, V., K. Tamura, et al. (2021). "Rapid suppression and sustained activation of distinct cortical regions for a delayed sensory-triggered motor response." Neuron 109(13): 2183-2201.e2189.

Fleming, W., S. Jewell, et al. (2021). "Inferring spikes from calcium imaging in dopamine neurons." PLOS ONE 16(6): e0252345. 10.1371/journal.pone.0252345

Fratzl, A., A. M. Koltchev, et al. (2021). "Flexible inhibitory control of visually evoked defensive behavior by the ventral lateral geniculate nucleus." Neuron 109(23): 3810-3822.e3819.

Gray Shawn, R., L. Ye, et al. "Noradrenergic terminal short-term potentiation enables modality-selective integration of sensory input and vigilance state." Science Advances 7(51): eabk1378. 10.1126/sciadv.abk1378

Kafashan, M., A. Jaffe, et al. (2020). "Scaling of information in large neural populations reveals signatures of information-limiting correlations." bioRxiv: 2020.2001.2010.902171. 10.1101/2020.01.10.902171

Keller, A. J., M. Dipoppa, et al. (2020). "A Disinhibitory Circuit for Contextual Modulation in Primary Visual Cortex." Neuron 108(6): 1181-1193.e1188.

Kline, A. M., D. A. Aponte, et al. (2021). "Inhibitory gating of coincidence-dependent sensory binding in secondary auditory cortex." Nature Communications 12(1): 4610. 10.1038/s41467-021-24758-6

Lee, J. S., J. J. Briguglio, et al. (2020). "The Statistical Structure of the Hippocampal Code for Space as a Function of Time, Context, and Value." Cell 183(3): 620-635.e622.

Lu, J., A. H. Behbahani, et al. (2022). "Transforming representations of movement from body- to world-centric space." Nature 601(7891): 98-104. 10.1038/s41586-021-04191-x

Lyall, E. H., D. P. Mossing, et al. (2021). "Synthesis of a comprehensive population code for contextual features in the awake sensory cortex." eLife 10: e62687. 10.7554/eLife.62687

Massengill, C. I., L. Bayless-Edwards, et al. (2021). "Highly sensitive genetically-encoded sensors for population and subcellular imaging of cAMP <em>in vivo</em&gt." bioRxiv: 2021.2008.2027.457999. 10.1101/2021.08.27.457999

Melander, J. B., A. Nayebi, et al. (2021). "Distinct in vivo dynamics of excitatory synapses onto cortical pyramidal neurons and parvalbumin-positive interneurons." Cell Reports 37(6): 109972.

Men, Y., L. Ye, et al. (2020). "Astroglial FMRP deficiency cell-autonomously up-regulates miR-128 and disrupts developmental astroglial mGluR5 signaling." Proceedings of the National Academy of Sciences 117(40): 25092. 10.1073/pnas.2014080117

Mittal, A. M., D. Gupta, et al. (2020). "Multiple network properties overcome random connectivity to enable stereotypic sensory responses." Nature Communications 11(1): 1023. 10.1038/s41467-020-14836-6

Orsolic, I., M. Rio, et al. (2021). "Mesoscale cortical dynamics reflect the interaction of sensory evidence and temporal expectation during perceptual decision-making." Neuron 109(11): 1861-1875.e1810.

Pacheco, D. A., S. Y. Thiberge, et al. (2021). "Auditory activity is diverse and widespread throughout the central brain of Drosophila." Nature Neuroscience 24(1): 93-104. 10.1038/s41593-020-00743-y

Perez-Alvarez, A., B. C. Fearey, et al. (2020). "Freeze-frame imaging of synaptic activity using SynTagMA." Nature Communications 11(1): 2464. 10.1038/s41467-020-16315-4

Pisano, F., M. Pisanello, et al. (2018). "Multipoint and large volume fiber photometry with a single tapered optical fiber implant." bioRxiv: 455766. 10.1101/455766

Porges, E., D. Jenner, et al. (2021). "Antibiotic-Loaded Polymersomes for Clearance of Intracellular Burkholderia thailandensis." ACS Nano 15(12): 19284-19297. 10.1021/acsnano.1c05309

Puścian, A., H. Benisty, et al. (2020). "NMDAR-Dependent Emergence of Behavioral Representation in Primary Visual Cortex." Cell Reports 32(4): 107970.

Scholl, B., D. E. Wilson, et al. (2019). "Functional Logic of Layer 2/3 Inhibitory Connectivity in the Ferret Visual Cortex." Neuron 104(3): 451-457.e453.

Schulze, L., J. Henninger, et al. (2018). "Transparent Danionella translucida as a genetically tractable vertebrate brain model." Nature Methods 15(11): 977-983. 10.1038/s41592-018-0144-6

Schumacher, J. W., M. McCann, et al. (2021). "Selective enhancement of neural coding in V1 underlies fine discrimination learning in tree shrew." bioRxiv: 2021.2001.2010.426145. 10.1101/2021.01.10.426145

Sedigh-Sarvestani, M., K.-S. Lee, et al. (2021). "A sinusoidal transform of the visual field in cortical area V2." bioRxiv: 2020.2012.2008.416651. 10.1101/2020.12.08.416651

Severson, K. S., D. Xu, et al. (2017). "Active Touch and Self-Motion Encoding by Merkel Cell-Associated Afferents." Neuron 94(3): 666-676.e669.

Shakhi, P. K., M. M. Bijeesh, et al. (2021). "An in-house constructed dual channel confocal fluorescence microscope for biomolecular imaging." OSA Continuum 4(8): 2177-2192. 10.1364/osac.428601

Stringer, C., M. Michaelos, et al. (2021). "High-precision coding in visual cortex." Cell 184(10): 2767-2778.e2715.

Sumser, A., M. Joesch, et al. (2021). "An extended toolkit for production and use of RVdG-CVS-N2c rabies viral vectors uncovers hidden hippocampal connections." bioRxiv: 2021.2012.2023.474014. 10.1101/2021.12.23.474014

Tang, L. and M. J. Higley (2020). "Layer 5 Circuits in V1 Differentially Control Visuomotor Behavior." Neuron 105(2): 346-354.e345.

Turner, N. L., T. Macrina, et al. (2020). "Multiscale and multimodal reconstruction of cortical structure and function." bioRxiv: 2020.2010.2014.338681. 10.1101/2020.10.14.338681

Unger, E. K., J. P. Keller, et al. (2020). "Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning." Cell 183(7): 1986-2002.e1926.

Vavladeli, A., T. Daigle, et al. (2020). "Projection-specific Activity of Layer 2/3 Neurons Imaged in Mouse Primary Somatosensory Barrel Cortex During a Whisker Detection Task." Function 1(1): zqaa008. 10.1093/function/zqaa008

Yang, W., M. Chini, et al. (2021). "Anesthetics fragment hippocampal network activity, alter spine dynamics, and affect memory consolidation." PLOS Biology 19(4): e3001146. 10.1371/journal.pbio.3001146

Yildirim, M., M. Hu, et al. (2019). "Label-free characterization of visual cortical areas in awake mice via three-photon microscopy reveals correlations between functional maps and structural substrates." bioRxiv: 790436. 10.1101/790436

Zhang, J.-F., B. Liu, et al. (2021). "An ultrasensitive biosensor for high-resolution kinase activity imaging in awake mice." Nature Chemical Biology 17(1): 39-46. 10.1038/s41589-020-00660-y

Zhang, K., J. Hu, et al. (2021). "Deep compressed imaging via optimized pattern scanning." Photonics Research 9(3): B57-B70. 10.1364/prj.410556

Zhao, Z., J. L. Zung, et al. (2020). "Chemical signatures of human odour generate a unique neural code in the brain of <em>Aedes aegypti</em> mosquitoes." bioRxiv: 2020.2011.2001.363861. 10.1101/2020.11.01.363861

Adam, E. M., T. Johns, et al. (2021). "Dynamic control of visually-guided locomotion through cortico-subthalamic projections." bioRxiv: 2020.2002.2005.936443. 10.1101/2020.02.05.936443

Allen, C. H., D. Ahmed, et al. (2021). "Label-free two-photon imaging of mitochondrial activity in murine macrophages stimulated with bacterial and viral ligands." Scientific Reports 11(1): 14081. 10.1038/s41598-021-93043-9

Aponte, D. A., G. Handy, et al. (2021). "Recurrent network dynamics shape direction selectivity in primary auditory cortex." Nature Communications 12(1): 314. 10.1038/s41467-020-20590-6

Arttamangkul, S., E. J. Platt, et al. (2021). "Functional independence of endogenous μ- and δ-opioid receptors co-expressed in cholinergic interneurons." eLife 10: e69740. 10.7554/eLife.69740

Arttamangkul, S., A. Plazek, et al. (2019). "Visualizing endogenous opioid receptors in living neurons using ligand-directed chemistry." eLife 8: e49319. 10.7554/eLife.49319

Chen, D., M. Ren, et al. (2020). "Design of a multi-modality DMD-based two-photon microscope system." Optics Express 28(20): 30187-30198. 10.1364/oe.404652

Efimova, V. S., L. V. Isaeva, et al. (2019). "Analysis of In Vivo Activity of the Bovine Cholesterol Hydroxylase/Lyase System Proteins Expressed in Escherichia coli." Molecular Biotechnology 61(4): 261-273. 10.1007/s12033-019-00158-6

Egger, R., Y. Tupikov, et al. (2020). "Local Axonal Conduction Shapes the Spatiotemporal Properties of Neural Sequences." Cell 183(2): 537-548.e512.

Haidey, J. N., G. Peringod, et al. (2021). "Astrocytes regulate ultra-slow arteriole oscillations via stretch-mediated TRPV4-COX-1 feedback." Cell Reports 36(5): 109405.

Herdzik, K. P., K. N. Bourdakos, et al. (2020). "Multimodal spectral focusing CARS and SFG microscopy with a tailored coherent continuum from a microstructured fiber." Applied Physics B 126(5): 84. 10.1007/s00340-020-7406-6

Hige, T., Y. Aso, et al. (2015). "Heterosynaptic Plasticity Underlies Aversive Olfactory Learning in Drosophila." Neuron 88(5): 985-998.

James, B., P. Piekarz, et al. (2021). "Multivesicular Release Increases the Efficiency of Information Transmission at Sensory Synapses." bioRxiv: 2021.2011.2004.467256. 10.1101/2021.11.04.467256

Ji, X., S. Saha, et al. (2017). "The Sodium Channel β4 Auxiliary Subunit Selectively Controls Long-Term Depression in Core Nucleus Accumbens Medium Spiny Neurons." Frontiers in Cellular Neuroscience 11. 10.3389/fncel.2017.00017

Kazemipour, A., O. Novak, et al. (2019). "Kilohertz frame-rate two-photon tomography." Nature Methods 16(8): 778-786. 10.1038/s41592-019-0493-9

Keller, A. J., M. M. Roth, et al. (2020). "Feedback generates a second receptive field in neurons of the visual cortex." Nature 582(7813): 545-549. 10.1038/s41586-020-2319-4

Kim, B., H. Le, et al. (2020). "High-speed combined reflectance confocal and moxifloxacin based two-photon microscopy." Biomedical Optics Express 11(3): 1555-1567. 10.1364/boe.385763

Kim, H., J. Homann, et al. (2019). "A Long Timescale Stimulus History Effect in the Primary Visual Cortex." bioRxiv: 585539. 10.1101/585539

Kim, S. S., A. M. Hermundstad, et al. (2019). "Generation of stable heading representations in diverse visual scenes." Nature 576(7785): 126-131. 10.1038/s41586-019-1767-1

Koekkoek, L. L., M. Slomp, et al. (2021). "Disruption of lateral hypothalamic calorie detection by a free choice high fat diet." The FASEB Journal 35(9): e21804.

Latifi, S., S. Mitchell, et al. (2020). "Neuronal Network Topology Indicates Distinct Recovery Processes after Stroke." Cerebral Cortex 30(12): 6363-6375. 10.1093/cercor/bhaa191

Liu, R., N. Ball, et al. (2019). "Aberration-free multi-plane imaging of neural activity from the mammalian brain using a fast-switching liquid crystal spatial light modulator." Biomedical Optics Express 10(10): 5059-5080. 10.1364/boe.10.005059

Liu, Y., G. Foustoukos, et al. (2022). "Axonal and Dendritic Morphology of Excitatory Neurons in Layer 2/3 Mouse Barrel Cortex Imaged Through Whole-Brain Two-Photon Tomography and Registered to a Digital Brain Atlas." Frontiers in neuroanatomy 15: 791015-791015. 10.3389/fnana.2021.791015

Liu, Y., Y. Xin, et al. (2021). "A cortical circuit mechanism for structural knowledge-based flexible sensorimotor decision-making." Neuron 109(12): 2009-2024.e2006.

Mahn, M., I. Saraf-Sinik, et al. (2021). "Optogenetic silencing of neurotransmitter release with a naturally occurring invertebrate rhodopsin." bioRxiv: 2021.2002.2018.431673. 10.1101/2021.02.18.431673

Moura, C. C., K. N. Bourdakos, et al. (2019). "Live-imaging of Bioengineered Cartilage Tissue using Multimodal Non-linear Molecular Imaging." Scientific Reports 9(1): 5561. 10.1038/s41598-019-41466-w

Oda, K., J. Vierock, et al. (2018). "Crystal structure of the red light-activated channelrhodopsin Chrimson." Nature Communications 9(1): 3949. 10.1038/s41467-018-06421-9

Perez-Alvarez, A., F. Huhn, et al. (2021). "Freeze-Frame Imaging of Dendritic Calcium Signals With TubuTag." Frontiers in Molecular Neuroscience 14. 10.3389/fnmol.2021.635820

Peron, S., R. Pancholi, et al. (2020). "Recurrent interactions in local cortical circuits." Nature 579(7798): 256-259. 10.1038/s41586-020-2062-x

Radvansky, B. A., J. Y. Oh, et al. (2021). "Behavior determines the hippocampal spatial mapping of a multisensory environment." Cell Reports 36(5): 109444.

Rikhye, R. V., M. Yildirim, et al. (2021). "Reliable Sensory Processing in Mouse Visual Cortex through Cooperative Interactions between Somatostatin and Parvalbumin Interneurons." The Journal of Neuroscience 41(42): 8761. 10.1523/jneurosci.3176-20.2021

Runyan, C. A., E. Piasini, et al. (2017). "Distinct timescales of population coding across cortex." Nature 548(7665): 92-96. 10.1038/nature23020

Shuster, S. A., M. J. Wagner, et al. (2021). "The relationship between birth timing, circuit wiring, and physiological response properties of cerebellar granule cells." Proceedings of the National Academy of Sciences 118(23): e2101826118. 10.1073/pnas.2101826118

Smith, G. B. and D. Fitzpatrick (2016). Viral Injection and Cranial Window Implantation for In Vivo Two-Photon Imaging. High-Resolution Imaging of Cellular Proteins: Methods and Protocols. S. D. Schwartzbach, O. Skalli and T. Schikorski. New York, NY, Springer New York: 171-185. 10.1007/978-1-4939-6352-2_10

Sridharan, S., M. A. Gajowa, et al. (2022). "High-performance microbial opsins for spatially and temporally precise perturbations of large neuronal networks." Neuron.

Streich, L., J. C. Boffi, et al. (2021). "High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy." Nature Methods 18(10): 1253-1258. 10.1038/s41592-021-01257-6

Takahashi, T., K. P. Herdzik, et al. (2021). "Selective Imaging of Microplastic and Organic Particles in Flow by Multimodal Coherent Anti-Stokes Raman Scattering and Two-Photon Excited Autofluorescence Analysis." Analytical Chemistry 93(12): 5234-5240. 10.1021/acs.analchem.0c05474

Tang, A. D., W. Bennett, et al. (2021). "Subthreshold repetitive transcranial magnetic stimulation drives structural synaptic plasticity in the young and aged motor cortex." Brain Stimulation 14(6): 1498-1507.

Tyson, A. L., M. Vélez-Fort, et al. (2022). "Accurate determination of marker location within whole-brain microscopy images." Scientific Reports 12(1): 867. 10.1038/s41598-021-04676-9

Valente, M., G. Pica, et al. (2021). "Correlations enhance the behavioral readout of neural population activity in association cortex." Nature Neuroscience 24(7): 975-986. 10.1038/s41593-021-00845-1

Wang, F., K. Wang, et al. (2020). "Circuit and Behavioral Mechanisms of Sexual Rejection by Drosophila Females." Current Biology 30(19): 3749-3760.e3743.

Wang, K., F. Wang, et al. (2021). "Neural circuit mechanisms of sexual receptivity in Drosophila females." Nature 589(7843): 577-581. 10.1038/s41586-020-2972-7

Xiong, W.-H., M. Qin, et al. (2021). "Myristoylation alone is sufficient for PKA catalytic subunits to associate with the plasma membrane to regulate neuronal functions." Proceedings of the National Academy of Sciences 118(15): e2021658118. 10.1073/pnas.2021658118

Yatsenko, D., T. Nguyen, et al. (2021). "DataJoint Elements: Data Workflows for Neurophysiology." bioRxiv: 2021.2003.2030.437358. 10.1101/2021.03.30.437358

Yildirim, M., H. Sugihara, et al. (2019). "Functional imaging of visual cortical layers and subplate in awake mice with optimized three-photon microscopy." Nature Communications 10(1): 177. 10.1038/s41467-018-08179-6

Yuhao, Y., S. Niraj, et al. (2020). Monitoring uptake of palmitic acid by glioma cells using stimulated Raman scattering microscopy. Proc.SPIE. 10.1117/12.2546260

Zhang, D., E. Redington, et al. (2021). "Rational engineering of ratiometric calcium sensors with bright green and red fluorescent proteins." Communications Biology 4(1): 924. 10.1038/s42003-021-02452-z

Zhou, A., S. A. Engelmann, et al. (2022). "Evaluation of resonant scanning as a high-speed imaging technique for two-photon imaging of cortical vasculature." Biomedical Optics Express 13(3): 1374-1385. 10.1364/boe.448473

Zhu, Y. and F. Gabbiani (2018). Combined Two-Photon Calcium Imaging and Single-Ommatidium Visual Stimulation to Study Fine-Scale Retinotopy in Insects. Extracellular Recording Approaches. R. V. Sillitoe. New York, NY, Springer New York: 185-206. 10.1007/978-1-4939-7549-5_10

Kim, S., M. L. Wallace, et al. (2022). "Co-packaging of opposing neurotransmitters in individual synaptic vesicles in the central nervous system." Neuron.

Lei, Z., K. Henderson, et al. (2022). "A neural circuit linking learning and sleep in Drosophila long-term memory." Nature Communications 13(1): 609.

Deschamps, J. and J. Ries (2020). "EMU: reconfigurable graphical user interfaces for Micro-Manager." BMC Bioinformatics 21(1): 456. 10.1186/s12859-020-03727-8

Fast, A., A. Lal, et al. (2020). "FLAME: Macroscopic imaging with microscopic resolution. Optical biopsy of human skin." bioRxiv: 2020.2001.2031.927590. 10.1101/2020.01.31.927590

Gaffield, M. A., S. B. Amat, et al. (2015). "Chronic imaging of movement-related Purkinje cell calcium activity in awake behaving mice." Journal of Neurophysiology 115(1): 413-422. 10.1152/jn.00834.2015

Gaffield, M. A. and J. M. Christie (2017). "Movement Rate Is Encoded and Influenced by Widespread, Coherent Activity of Cerebellar Molecular Layer Interneurons." The Journal of Neuroscience 37(18): 4751. 10.1523/jneurosci.0534-17.2017

Gill, J. V., G. M. Lerman, et al. (2020). "Precise Holographic Manipulation of Olfactory Circuits Reveals Coding Features Determining Perceptual Detection." Neuron 108(2): 382-393.e385.

Giovannucci, A., A. Badura, et al. (2017). "Cerebellar granule cells acquire a widespread predictive feedback signal during motor learning." Nature Neuroscience 20(5): 727-734. 10.1038/nn.4531

Graves, A. R., R. H. Roth, et al. (2021). "Visualizing synaptic plasticity in vivo by large-scale imaging of endogenous AMPA receptors." eLife 10: e66809. 10.7554/eLife.66809

Griffiths, V. A., A. M. Valera, et al. (2020). "Real-time 3D movement correction for two-photon imaging in behaving animals." Nature Methods 17(7): 741-748. 10.1038/s41592-020-0851-7

Henschke, J. U., E. Dylda, et al. (2020). "Reward Association Enhances Stimulus-Specific Representations in Primary Visual Cortex." Current Biology 30(10): 1866-1880.e1865.

Jayant, K., J. J. Hirtz, et al. (2017). "Targeted intracellular voltage recordings from dendritic spines using quantum-dot-coated nanopipettes." Nature Nanotechnology 12(4): 335-342. 10.1038/nnano.2016.268

Ji, X., S. Saha, et al. (2017). "Dopamine Receptors Differentially Control Binge Alcohol Drinking-Mediated Synaptic Plasticity of the Core Nucleus Accumbens Direct and Indirect Pathways." The Journal of Neuroscience 37(22): 5463. 10.1523/jneurosci.3845-16.2017

Kim Sung, S., H. Rouault, et al. (2017). "Ring attractor dynamics in the Drosophila central brain." Science 356(6340): 849-853. 10.1126/science.aal4835

Klioutchnikov, A., D. J. Wallace, et al. (2020). "Three-photon head-mounted microscope for imaging deep cortical layers in freely moving rats." Nature Methods 17(5): 509-513. 10.1038/s41592-020-0817-9

Li, B., C. Wu, et al. (2020). "An adaptive excitation source for high-speed multiphoton microscopy." Nature Methods 17(2): 163-166. 10.1038/s41592-019-0663-9

Liu, H., Y. Du, et al. (2017). "Sealing of Immersion Deuterium Dioxide and Its Application to Signal Maintenance for Ex-Vivo and In-Vivo Multiphoton Microscopy Excited at the 1700-nm Window." IEEE Photonics Journal 9(5): 1-8. 10.1109/jphot.2017.2737012

Liu, H., J. Wang, et al. (2018). "Ex and in vivo characterization of the wavelength-dependent 3-photon action cross-sections of red fluorescent proteins covering the 1700-nm window." Journal of Biophotonics 11(7): e201700351.

Liu, R., N. Ball, et al. (2018). "Multi-plane Imaging of Neural Activity From the Mammalian Brain Using a Fast-switching Liquid Crystal Spatial Light Modulator." bioRxiv: 506618. 10.1101/506618

Liu, R., Z. Li, et al. (2019). "Direct wavefront sensing enables functional imaging of infragranular axons and spines." Nature Methods 16(7): 615-618. 10.1038/s41592-019-0434-7

Ma, Z., H. Liu, et al. (2020). "Stability of motor cortex network states during learning-associated neural reorganizations." Journal of Neurophysiology 124(5): 1327-1342. 10.1152/jn.00061.2020

Marvin, J. S., B. Scholl, et al. (2018). "Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR." Nature Methods 15(11): 936-939. 10.1038/s41592-018-0171-3

Mitani, A. and T. Komiyama (2018). "Real-Time Processing of Two-Photon Calcium Imaging Data Including Lateral Motion Artifact Correction." Frontiers in Neuroinformatics 12. 10.3389/fninf.2018.00098

Moran, A. K., T. P. Eiting, et al. (2021). "Dynamics of Glutamatergic Drive Underlie Diverse Responses of Olfactory Bulb Outputs In Vivo." eNeuro 8(2): ENEURO.0110-0121.2021. 10.1523/eneuro.0110-21.2021

Pafundo, D. E., M. A. Nicholas, et al. (2016). "Top-Down-Mediated Facilitation in the Visual Cortex Is Gated by Subcortical Neuromodulation." The Journal of Neuroscience 36(10): 2904. 10.1523/jneurosci.2909-15.2016

Pisanello, M., F. Pisano, et al. (2019). "The Three-Dimensional Signal Collection Field for Fiber Photometry in Brain Tissue." Frontiers in Neuroscience 13. 10.3389/fnins.2019.00082

Pologruto, T. A., B. L. Sabatini, et al. (2003). "ScanImage: Flexible software for operating laser scanning microscopes." BioMedical Engineering OnLine 2(1): 13. 10.1186/1475-925x-2-13

Pottackal, J., J. H. Singer, et al. (2021). "Computational and Molecular Properties of Starburst Amacrine Cell Synapses Differ With Postsynaptic Cell Type." Frontiers in Cellular Neuroscience 15. 10.3389/fncel.2021.660773

Reimer, J., M. J. McGinley, et al. (2016). "Pupil fluctuations track rapid changes in adrenergic and cholinergic activity in cortex." Nature Communications 7(1): 13289. 10.1038/ncomms13289

Song, A., A. S. Charles, et al. (2017). "Volumetric two-photon imaging of neurons using stereoscopy (vTwINS)." Nature Methods 14(4): 420-426. 10.1038/nmeth.4226

Takasaki, K. T., D. Tsyboulski, et al. (2019). "Dual-plane 3-photon microscopy with remote focusing." Biomedical Optics Express 10(11): 5585-5599. 10.1364/boe.10.005585

Thomas, C. I., M. A. Ryan, et al. (2021). "Targeting Functionally Characterized Synaptic Architecture Using Inherent Fiducials and 3D Correlative Microscopy." Microscopy and Microanalysis 27(1): 156-169. Doi: 10.1017/s1431927620024757

Valle, A. F. and J. D. Seelig (2019). "Two-photon Bessel beam tomography for fast volume imaging." Optics Express 27(9): 12147-12162. 10.1364/oe.27.012147

Wagner, M. J., J. Savall, et al. (2021). "A neural circuit state change underlying skilled movements." Cell 184(14): 3731-3747.e3721.

Wang, K., Y. Pan, et al. (2021). "Deep-skin multiphoton microscopy of lymphatic vessels excited at the 1700-nm window in vivo." Biomedical Optics Express 12(10): 6474-6484. 10.1364/boe.437482

Wang, K., W. Wen, et al. (2017). "Order-of-magnitude multiphoton signal enhancement based on characterization of absorption spectra of immersion oils at the 1700-nm window." Optics Express 25(6): 5909-5916. 10.1364/oe.25.005909

Yildirim, M., M. Hu, et al. (2020). "Quantitative third-harmonic generation imaging of mouse visual cortex areas reveals correlations between functional maps and structural substrates." Biomedical Optics Express 11(10): 5650-5673. 10.1364/boe.396962

Yu, C.-H., J. N. Stirman, et al. (2021). "Diesel2p mesoscope with dual independent scan engines for flexible capture of dynamics in distributed neural circuitry." Nature Communications 12(1): 6639. 10.1038/s41467-021-26736-4

Dhanya, S. K. and G. Hasan (2022). "Two photon imaging of calcium responses in murine Purkinje neurons." STAR Protocols 3(1): 101105.

Tyson, A. L., M. Vélez-Fort, et al. (2022). "Accurate determination of marker location within whole-brain microscopy images." Scientific Reports 12(1): 867.

Hartveit, E., M. L. Veruki, et al. (2022). "Dendritic morphology of an inhibitory retinal interneuron enables simultaneous local and global synaptic integration." The Journal of Neuroscience: JN-RM-0695-0621.

Sun, B., M. Wang, et al. (2022). "Intravital Imaging of the Murine Subventricular Zone with Three Photon Microscopy." Cerebral Cortex: bhab400.

Pulin, M., K. E. Stockhausen, et al. (2022). "Orthogonally-polarized excitation for improved two-photon and second-harmonic-generation microscopy, applied to neurotransmitter imaging with GPCR-based sensors." Biomedical Optics Express 13(2): 777-790.

Tiriac, A., K. Bistrong, et al. (2022). "The influence of spontaneous and visual activity on the development of direction selectivity maps in mouse retina." Cell Reports 38(2): 110225.

Ueda, H. H., Y. Nagasawa, et al. (2022). "Chronic neuronal excitation leads to dual metaplasticity in the signaling for structural long-term potentiation." Cell Reports 38(1): 110153.

Tsukahara, T., D. H. Brann, et al. (2021). "A transcriptional rheostat couples past activity to future sensory responses." Cell.

Heuke, S., I. Rimke, et al. (2021). "Shot-noise limited tunable dual-vibrational frequency stimulated Raman scattering microscopy." Biomedical Optics Express 12(12): 7780-7789.

Zhuang, J., Y. Wang, et al. (2021). "Laminar distribution and arbor density of two functional classes of thalamic inputs to primary visual cortex." Cell Reports 37(2): 109826.

Fratzl, A., A. M. Koltchev, et al. (2021). "Flexible inhibitory control of visually evoked defensive behavior by the ventral lateral geniculate nucleus." Neuron.

Abdolghader, P., A. Ridsdale, et al. (2021). "Unsupervised hyperspectral stimulated Raman microscopy image enhancement: denoising and segmentation via one-shot deep learning." Optics Express 29(21): 34205-34219.

Goltstein, P. M., S. Reinert, et al. (2021). "Mouse visual cortex areas represent perceptual and semantic features of learned visual categories." Nature Neuroscience 24(10): 1441-1451.

Wang, K., Y. Pan, et al. (2021). "Deep-skin multiphoton microscopy of lymphatic vessels excited at the 1700-nm window in vivo." Biomedical Optics Express 12(10): 6474-6484.

Agrawal, S., Dickinson, E. S., Sustar, A., Gurung, P., Shepherd, D., Truman, J. W., & Tuthill, J. C. (2020). Central processing of leg proprioception in Drosophila. eLife, 9, e60299. doi: 10.7554/eLife.60299.

Allen, C. H., Ahmed, D., Raiche-Tanner, O., Chauhan, V., Mostaço-Guidolin, L., Cassol, E., & Murugkar, S. (2021). Label-free two-photon imaging of mitochondrial activity in murine macrophages stimulated with bacterial and viral ligands. Scientific Reports, 11(1), 14081. doi: 10.1038/s41598-021-93043-9.

Allen, C. H., Benjamin, H., Olivia, R.-T., & Sangeeta, M. (2021). Compact silicon photomultiplier detection of multimodal multiphoton microscopy signals. Paper presented at the Proc.SPIE.

Allen, C. H., Hansson, B., Raiche-Tanner, O., & Murugkar, S. (2020). Coherent anti-Stokes Raman scattering imaging using silicon photomultipliers. Optics Letters, 45(8), 2299-2302. doi: 10.1364/ol.390050.

Arttamangkul, S., Plazek, A., Platt, E. J., Jin, H., Murray, T. F., Birdsong, W. T., . . . Williams, J. T. (2019). Visualizing endogenous opioid receptors in living neurons using ligand-directed chemistry. eLife, 8, e49319. doi: 10.7554/eLife.49319.

Aso, Y., Ray, R. P., Long, X., Bushey, D., Cichewicz, K., Ngo, T.-T. B., . . . Rubin, G. M. (2019). Nitric oxide acts as a cotransmitter in a subset of dopaminergic neurons to diversify memory dynamics. eLife, 8, e49257. doi: 10.7554/eLife.49257.

Bale, M. R., Bitzidou, M., Giusto, E., Kinghorn, P., & Maravall, M. (2021). Sequence Learning Induces Selectivity to Multiple Task Parameters in Mouse Somatosensory Cortex. Current Biology, 31(3), 473-485.e475. doi:

Benbenishty, A., Gadrich, M., Cottarelli, A., Lubart, A., Kain, D., Amer, M., . . . Blinder, P. (2019). Prophylactic TLR9 stimulation reduces brain metastasis through microglia activation. PLOS Biology, 17(3), e2006859. doi: 10.1371/journal.pbio.2006859.

Bjørnstad, D. M., Åbjørsbråten, K. S., Hennestad, E., Cunen, C., Hermansen, G. H., Bojarskaite, L., . . . Enger, R. (2021). Begonia—A Two-Photon Imaging Analysis Pipeline for Astrocytic Ca2+ Signals. [Original Research]. Frontiers in cellular neuroscience, 15(176). doi: 10.3389/fncel.2021.681066.

Blot, A., Roth, M. M., Gasler, I., Javadzadeh, M., Imhof, F., & Hofer, S. B. (2021). Visual intracortical and transthalamic pathways carry distinct information to cortical areas. Neuron, 109(12), 1996-2008.e1996. doi:

Chakraborty, T., Chen, B., Daetwyler, S., Chang, B.-J., Vanderpoorten, O., Sapoznik, E., . . . Fiolka, R. (2020). Converting lateral scanning into axial focusing to speed up three-dimensional microscopy. Light: Science & Applications, 9(1), 165. doi: 10.1038/s41377-020-00401-9.

Chang, J. T., Whitney, D., & Fitzpatrick, D. (2020). Experience-Dependent Reorganization Drives Development of a Binocularly Unified Cortical Representation of Orientation. Neuron, 107(2), 338-350.e335. doi:

Chen, B., Chakraborty, T., Daetwyler, S., Manton, J. D., Dean, K., & Fiolka, R. (2020). Extended depth of focus multiphoton microscopy via incoherent pulse splitting. Biomedical Optics Express, 11(7), 3830-3842. doi: 10.1364/boe.393931.

Chen, D., Ren, M., Zhang, D., Chen, J., Gu, S., & Chen, S.-C. (2020). Design of a multi-modality DMD-based two-photon microscope system. Optics Express, 28(20), 30187-30198. doi: 10.1364/oe.404652.

Chen, X., Cheng, H., Deng, X., Tong, S., Li, J., Qiu, P., & Wang, K. (2021). Self-phase-modulated femtosecond laser source at 1603 nm and its application to deep-brain 3-photon microscopy in vivo. []. Journal of Biophotonics, 14(3), e202000349. doi:

Cheng, H., Tong, S., Deng, X., Liu, H., Du, Y., He, C., . . . Wang, K. (2019). Deep-brain 2-photon fluorescence microscopy in vivo excited at the1700  nm window. Optics Letters, 44(17), 4432-4435. doi: 10.1364/ol.44.004432.

Cheung, J., Maire, P., Kim, J., Sy, J., & Hires, S. A. (2019). The Sensorimotor Basis of Whisker-Guided Anteroposterior Object Localization in Head-Fixed Mice. Current Biology, 29(18), 3029-3040.e3024. doi:

Choi, J., Goncharov, V., Kleinbart, J., Orsborn, A., & Pesaran, B. (2018, 18-21 July 2018). Monkey-MIMMS: Towards Automated Cellular Resolution Large- Scale Two-Photon Microscopy In The Awake Macaque Monkey. Paper presented at the 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).

Chong, E. Z., Panniello, M., Barreiros, I., Kohl, M. M., & Booth, M. J. (2019). Quasi-simultaneous multiplane calcium imaging of neuronal circuits. Biomedical Optics Express, 10(1), 267-282. doi: 10.1364/boe.10.000267.

Clemens, J., Ozeri-Engelhard, N., & Murthy, M. (2018). Fast intensity adaptation enhances the encoding of sound in Drosophila. Nature Communications, 9(1), 134. doi: 10.1038/s41467-017-02453-9.

Collot, M., Wilms, C. D., Bentkhayet, A., Marcaggi, P., Couchman, K., Charpak, S., . . . Mallet, J.-M. (2015). CaRuby-Nano: a novel high affinity calcium probe for dual color imaging. eLife, 4, e05808. doi: 10.7554/eLife.05808.

Costa Moura, C., Lanham, S. A., Monfort, T., Bourdakos, K. N., Tare, R. S., Oreffo, R. O. C., & Mahajan, S. (2018). Quantitative temporal interrogation in 3D of bioengineered human cartilage using multimodal label-free imaging. Integrative Biology, 10(10), 635-645. doi: 10.1039/c8ib00050f.

Dag, U., Lei, Z., Le, J. Q., Wong, A., Bushey, D., & Keleman, K. (2019). Neuronal reactivation during post-learning sleep consolidates long-term memory in Drosophila. eLife, 8, e42786. doi: 10.7554/eLife.42786.

Dana, H., Sun, Y., Mohar, B., Hulse, B. K., Kerlin, A. M., Hasseman, J. P., . . . Kim, D. S. (2019). High-performance calcium sensors for imaging activity in neuronal populations and microcompartments. Nature Methods, 16(7), 649-657. doi: 10.1038/s41592-019-0435-6.

de Boer, W. D. A. M., Hirtz, J. J., Capretti, A., Gregorkiewicz, T., Izquierdo-Serra, M., Han, S., . . . Yuste, R. (2018). Neuronal photoactivation through second-harmonic near-infrared absorption by gold nanoparticles. Light: Science & Applications, 7(1), 100. doi: 10.1038/s41377-018-0103-0.

de Malmazet, D., Kühn, N. K., & Farrow, K. (2018). Retinotopic Separation of Nasal and Temporal Motion Selectivity in the Mouse Superior Colliculus. Current Biology, 28(18), 2961-2969.e2964. doi:

Deverett, B., Koay, S. A., Oostland, M., & Wang, S. S. H. (2018). Cerebellar involvement in an evidence-accumulation decision-making task. eLife, 7, e36781. doi: 10.7554/eLife.36781.

Diana, G., Sainsbury, T. T. J., & Meyer, M. P. (2019). Bayesian inference of neuronal assemblies. PLOS Computational Biology, 15(10), e1007481. doi: 10.1371/journal.pcbi.1007481.

Donzis, E. J., Estrada-Sánchez, A. M., Indersmitten, T., Oikonomou, K., Tran, C. H., Wang, C., . . . Levine, M. S. (2020). Cortical Network Dynamics Is Altered in Mouse Models of Huntington’s Disease. Cerebral Cortex, 30(4), 2372-2388. doi: 10.1093/cercor/bhz245.

Driscoll, L. N., Pettit, N. L., Minderer, M., Chettih, S. N., & Harvey, C. D. (2017). Dynamic Reorganization of Neuronal Activity Patterns in Parietal Cortex. Cell, 170(5), 986-999.e916. doi:

Dürst, C. D., Wiegert, J. S., Helassa, N., Kerruth, S., Coates, C., Schulze, C., . . . Oertner, T. G. (2019). High-speed imaging of glutamate release with genetically encoded sensors. Nature Protocols, 14(5), 1401-1424. doi: 10.1038/s41596-019-0143-9.

El-Boustani, S., Sermet, B. S., Foustoukos, G., Oram, T. B., Yizhar, O., & Petersen, C. C. H. (2020). Anatomically and functionally distinct thalamocortical inputs to primary and secondary mouse whisker somatosensory cortices. Nature Communications, 11(1), 3342. doi: 10.1038/s41467-020-17087-7.

Engelhard, B., Finkelstein, J., Cox, J., Fleming, W., Jang, H. J., Ornelas, S., . . . Witten, I. B. (2019). Specialized coding of sensory, motor and cognitive variables in VTA dopamine neurons. Nature, 570(7762), 509-513. doi: 10.1038/s41586-019-1261-9.

Esmaeili, V., Tamura, K., Muscinelli, S. P., Modirshanechi, A., Boscaglia, M., Lee, A. B., . . . Petersen, C. C. H. (2021). Rapid suppression and sustained activation of distinct cortical regions for a delayed sensory-triggered motor response. Neuron, 109(13), 2183-2201.e2189. doi:

Euler, T., Franke, K., & Baden, T. (2019). Studying a Light Sensor with Light: Multiphoton Imaging in the Retina. In E. Hartveit (Ed.), Multiphoton Microscopy (pp. 225-250). New York, NY: Springer New York.

Fast, A., Lal, A., Durkin, A. F., Lentsch, G., Harris, R. M., Zachary, C. B., . . . Balu, M. (2020). Fast, large area multiphoton exoscope (FLAME) for macroscopic imaging with microscopic resolution of human skin. Scientific Reports, 10(1), 18093. doi: 10.1038/s41598-020-75172-9.

Fast, A., Lal, A., Durkin, A. F., Zachary, C. B., Ganesan, A. K., & Balu, M. (2020). FLAME: Macroscopic imaging with microscopic resolution. Optical biopsy of human skin. bioRxiv, 2020.2001.2031.927590. doi: 10.1101/2020.01.31.927590.

Feese, B. D., Pafundo, D. E., Schmehl, M. N., & Kuhlman, S. J. (2017). Binocular deprivation induces both age-dependent and age-independent forms of plasticity in parvalbumin inhibitory neuron visual response properties. Journal of Neurophysiology, 119(2), 738-751. doi: 10.1152/jn.00386.2017.

Fleming, W., Jewell, S., Engelhard, B., Witten, D. M., & Witten, I. B. (2021). Inferring spikes from calcium imaging in dopamine neurons. PLOS ONE, 16(6), e0252345. doi: 10.1371/journal.pone.0252345.

Gaffield, M. A., Amat, S. B., Bito, H., & Christie, J. M. (2016). Chronic imaging of movement-related Purkinje cell calcium activity in awake behaving mice. Journal of Neurophysiology, 115(1), 413-422. doi: 10.1152/jn.00834.2015.

Gaffield, M. A., Bonnan, A., & Christie, J. M. (2019). Conversion of Graded Presynaptic Climbing Fiber Activity into Graded Postsynaptic Ca2+ Signals by Purkinje Cell Dendrites. Neuron, 102(4), 762-769.e764. doi:

Gaffield, M. A., & Christie, J. M. (2017). Movement Rate Is Encoded and Influenced by Widespread, Coherent Activity of Cerebellar Molecular Layer Interneurons. The Journal of Neuroscience, 37(18), 4751. doi: 10.1523/jneurosci.0534-17.2017.

Gaffield, M. A., Rowan, M. J. M., Amat, S. B., Hirai, H., & Christie, J. M. (2018). Inhibition gates supralinear Ca2+ signaling in Purkinje cell dendrites during practiced movements. eLife, 7, e36246. doi: 10.7554/eLife.36246.

Gala, R., Lebrecht, D., Sahlender, D. A., Jorstad, A., Knott, G., Holtmaat, A., & Stepanyants, A. (2017). Computer assisted detection of axonal bouton structural plasticity in in vivo time-lapse images. eLife, 6, e29315. doi: 10.7554/eLife.29315.

Gan, M., He, C., Liu, H., Zhuang, Z., Qiu, P., & Wang, K. (2019). Air-core fiber or photonic-crystal rod, which is more suitable for energetic femtosecond pulse generation and three-photon microscopy at the 1700-nm window? []. Journal of Biophotonics, 12(10), e201900069. doi:

Gauthier, J. L., & Tank, D. W. (2018). A Dedicated Population for Reward Coding in the Hippocampus. Neuron, 99(1), 179-193.e177. doi:

Godenzini, L., Alwis, D., Guzulaitis, R., Honnuraiah, S., Stuart, G. J., & Palmer, L. M. (2021). Auditory input enhances somatosensory encoding and tactile goal-directed behavior. Nature Communications, 12(1), 4509. doi: 10.1038/s41467-021-24754-w.

Groschner, L. N., Chan Wah Hak, L., Bogacz, R., DasGupta, S., & Miesenböck, G. (2018). Dendritic Integration of Sensory Evidence in Perceptual Decision-Making. Cell, 173(4), 894-905.e813. doi:

Gu, Y., Lewallen, S., Kinkhabwala, A. A., Domnisoru, C., Yoon, K., Gauthier, J. L., . . . Tank, D. W. (2018). A Map-like Micro-Organization of Grid Cells in the Medial Entorhinal Cortex. Cell, 175(3), 736-750.e730. doi:

Hall, C. E., McNamara, J. O., & Yasuda, R. (2019). Analysis of TrkB Receptor Activity Using FRET Sensors. In C. B. Duarte & E. Tongiorgi (Eds.), Brain-Derived Neurotrophic Factor (BDNF) (pp. 149-157). New York, NY: Springer New York.

Hamodi, A. S., Martinez Sabino, A., Fitzgerald, N. D., Moschou, D., & Crair, M. C. (2020). Transverse sinus injections drive robust whole-brain expression of transgenes. eLife, 9, e53639. doi: 10.7554/eLife.53639.

Hamodi, A. S., Sabino, A. M., Fitzgerald, N. D., & Crair, M. C. (2019). Transverse sinus injections: A novel method for whole-brain vector-driven gene delivery. bioRxiv, 579730. doi: 10.1101/579730.

Har-Gil, H., Golgher, L., Israel, S., Kain, D., Cheshnovsky, O., Parnas, M., & Blinder, P. (2018). PySight: plug and play photon counting for fast continuous volumetric intravital microscopy. Optica, 5(9), 1104-1112. doi: 10.1364/optica.5.001104.

Hattori, R., Danskin, B., Babic, Z., Mlynaryk, N., & Komiyama, T. (2019). Area-Specificity and Plasticity of History-Dependent Value Coding During Learning. Cell, 177(7), 1858-1872.e1815. doi:

He, C., Deng, X., Pan, Y., Tong, S., Kang, J., Li, J., . . . Wang, K. (2020). 3-photon microscopy of myelin in mouse digital skin excited at the 1700-nm window. []. Journal of Biophotonics, 13(12), e202000321. doi:

He, C., Gan, M., Deng, X., Liu, H., Qiu, P., & Wang, K. (2019). 3-photon fluorescence imaging of sulforhodamine B-labeled elastic fibers in the mouse skin in vivo. []. Journal of Biophotonics, 12(11), e201900185. doi:

He, J., Du, Y., Zhuang, Z., Wen, W., Liu, H., Wang, K., & Qiu, P. (2018). Wavelength Separation Tunable 2-Color Soliton Generation and Its Application to 2-Color Fluorescence Multiphoton Microscopy. Journal of Lightwave Technology, 36(16), 3249-3253. doi: 10.1109/jlt.2018.2833280. 

Henschke, J. U., Dylda, E., Katsanevaki, D., Dupuy, N., Currie, S. P., Amvrosiadis, T., . . . Rochefort, N. L. (2020). Reward Association Enhances Stimulus-Specific Representations in Primary Visual Cortex. Current Biology, 30(10), 1866-1880.e1865. doi:

Henschke, J. U., Price, A. T., & Pakan, J. M. P. (2021). Enhanced modulation of cell-type specific neuronal responses in mouse dorsal auditory field during locomotion. Cell Calcium, 96, 102390. doi:

Herdzik, K. P., Bourdakos, K. N., Johnson, P. B., Lister, A. P., Pitera, A. P., Guo, C.-y., . . . Mahajan, S. (2020). Multimodal spectral focusing CARS and SFG microscopy with a tailored coherent continuum from a microstructured fiber. Applied Physics B, 126(5), 84. doi: 10.1007/s00340-020-7406-6.

Hige, T., Aso, Y., Modi, Mehrab N., Rubin, Gerald M., & Turner, Glenn C. (2015). Heterosynaptic Plasticity Underlies Aversive Olfactory Learning in Drosophila. Neuron, 88(5), 985-998. doi:

Inoue, M., Takeuchi, A., Manita, S., Horigane, S.-i., Sakamoto, M., Kawakami, R., . . . Bito, H. (2019). Rational Engineering of XCaMPs, a Multicolor GECI Suite for In Vivo Imaging of Complex Brain Circuit Dynamics. Cell, 177(5), 1346-1360.e1324. doi:

Jackman, S. L., Chen, C. H., Chettih, S. N., Neufeld, S. Q., Drew, I. R., Agba, C. K., . . . Regehr, W. G. (2018). Silk Fibroin Films Facilitate Single-Step Targeted Expression of Optogenetic Proteins. Cell Reports, 22(12), 3351-3361. doi:

Jeanne, J. M., Fişek, M., & Wilson, R. I. (2018). The Organization of Projections from Olfactory Glomeruli onto Higher-Order Neurons. Neuron, 98(6), 1198-1213.e1196. doi:

Kafashan, M., Jaffe, A. W., Chettih, S. N., Nogueira, R., Arandia-Romero, I., Harvey, C. D., . . . Drugowitsch, J. (2021). Scaling of sensory information in large neural populations shows signatures of information-limiting correlations. Nature Communications, 12(1), 473. doi: 10.1038/s41467-020-20722-y.

Katlowitz, K. A., Picardo, M. A., & Long, M. A. (2018). Stable Sequential Activity Underlying the Maintenance of a Precisely Executed Skilled Behavior. Neuron, 98(6), 1133-1140.e1133. doi:

Kato, H. K., Asinof, S. K., & Isaacson, J. S. (2017). Network-Level Control of Frequency Tuning in Auditory Cortex. Neuron, 95(2), 412-423.e414. doi:

Kato, Hiroyuki K., Gillet, Shea N., & Isaacson, Jeffry S. (2015). Flexible Sensory Representations in Auditory Cortex Driven by Behavioral Relevance. Neuron, 88(5), 1027-1039. doi:

Kerlin, A., Mohar, B., Flickinger, D., MacLennan, B. J., Dean, M. B., Davis, C., . . . Svoboda, K. (2019). Functional clustering of dendritic activity during decision-making. eLife, 8, e46966. doi: 10.7554/eLife.46966.

Kim, H., Homann, J., Tank, D. W., & Berry, M. J. (2019). A Long Timescale Stimulus History Effect in the Primary Visual Cortex. bioRxiv, 585539. doi: 10.1101/585539.

Kim, M.-H., Znamenskiy, P., Iacaruso, M. F., & Mrsic-Flogel, T. D. (2018). Segregated Subnetworks of Intracortical Projection Neurons in Primary Visual Cortex. Neuron, 100(6), 1313-1321.e1316. doi:

Kinkhabwala, A. A., Gu, Y., Aronov, D., & Tank, D. W. (2020). Visual cue-related activity of cells in the medial entorhinal cortex during navigation in virtual reality. eLife, 9, e43140. doi: 10.7554/eLife.43140.

Klapoetke, N. C., Nern, A., Peek, M. Y., Rogers, E. M., Breads, P., Rubin, G. M., . . . Card, G. M. (2017). Ultra-selective looming detection from radial motion opponency. Nature, 551(7679), 237-241. doi: 10.1038/nature24626.

Knoblich, U., Huang, L., Zeng, H., & Li, L. (2019). Neuronal cell-subtype specificity of neural synchronization in mouse primary visual cortex. Nature Communications, 10(1), 2533. doi: 10.1038/s41467-019-10498-1.

Lee, K.-S., Huang, X., & Fitzpatrick, D. (2016). Topology of ON and OFF inputs in visual cortex enables an invariant columnar architecture. Nature, 533(7601), 90-94. doi: 10.1038/nature17941.

LeMessurier, A. M., Laboy-Juárez, K. J., McClain, K., Chen, S., Nguyen, T., & Feldman, D. E. (2019). Enrichment drives emergence of functional columns and improves sensory coding in the whisker map in L2/3 of mouse S1. eLife, 8, e46321. doi: 10.7554/eLife.46321.

Lerman, G. M., Little, J. P., Gill, J. V., Rinberg, D., & Shoham, S. (2019). Real-Time In Situ Holographic Optogenetics Confocally Unraveled Sculpting Microscopy. []. Laser & Photonics Reviews, 13(9), 1900144. doi:

Light, S. E. W., & Jontes, J. D. (2019). Multiplane Calcium Imaging Reveals Disrupted Development of Network Topology in Zebrafish pcdh19 Mutants. eNeuro, 6(3), ENEURO.0420-0418.2019. doi: 10.1523/eneuro.0420-18.2019.

Lin, Q., Manley, J., Helmreich, M., Schlumm, F., Li, J. M., Robson, D. N., . . . Vaziri, A. (2020). Cerebellar Neurodynamics Predict Decision Timing and Outcome on the Single-Trial Level. Cell, 180(3), 536-551.e517. doi:

Liu, H., Du, Y., Peng, X., Zhou, X., Qiu, P., & Wang, K. (2017). Sealing of Immersion Deuterium Dioxide and Its Application to Signal Maintenance for Ex-Vivo and In-Vivo Multiphoton Microscopy Excited at the 1700-nm Window. IEEE Photonics Journal, 9(5), 1-8. doi: 10.1109/jphot.2017.2737012. 

Liu, H., Zhuang, Z., He, J., Tong, S., He, C., Deng, X., . . . Wang, K. (2019). High-energy polarized soliton synthesis and its application to deep-brain 3-photon microscopy in vivo. Optics Express, 27(11), 15309-15317. doi: 10.1364/oe.27.015309.

Liu, R., Ball, N., Brockill, J., Kuan, L., Millman, D., White, C., . . . Saggau, P. (2018). Multi-plane Imaging of Neural Activity From the Mammalian Brain Using a Fast-switching Liquid Crystal Spatial Light Modulator. bioRxiv, 506618. doi: 10.1101/506618.

Long, B., Li, L., Knoblich, U., Zeng, H., & Peng, H. (2015). 3D Image-Guided Automatic Pipette Positioning for Single Cell Experiments in vivo. Scientific Reports, 5(1), 18426. doi: 10.1038/srep18426.

Lur, G., Vinck, Martin A., Tang, L., Cardin, Jessica A., & Higley, Michael J. (2016). Projection-Specific Visual Feature Encoding by Layer 5 Cortical Subnetworks. Cell Reports, 14(11), 2538-2545. doi:

Ma, L., Jongbloets, B. C., Xiong, W.-H., Melander, J. B., Qin, M., Lameyer, T. J., . . . Zhong, H. (2018). A Highly Sensitive A-Kinase Activity Reporter for Imaging Neuromodulatory Events in Awake Mice. Neuron, 99(4), 665-679.e665. doi:

Ma, Z., Liu, H., Komiyama, T., & Wessel, R. (2020). Stability of motor cortex network states during learning-associated neural reorganizations. Journal of Neurophysiology, 124(5), 1327-1342. doi: 10.1152/jn.00061.2020.

Makino, H., Ren, C., Liu, H., Kim, A. N., Kondapaneni, N., Liu, X., . . . Komiyama, T. (2017). Transformation of Cortex-wide Emergent Properties during Motor Learning. Neuron, 94(4), 880-890.e888. doi:

Maltese, M., March, J. R., Bashaw, A. G., & Tritsch, N. X. (2019). Dopamine modulates the size of striatal projection neuron ensembles. bioRxiv, 865006. doi: 10.1101/865006.

Maltese, M., March, J. R., Bashaw, A. G., & Tritsch, N. X. (2021). Dopamine differentially modulates the size of projection neuron ensembles in the intact and dopamine-depleted striatum. eLife, 10, e68041. doi: 10.7554/eLife.68041.

Mamiya, A., Gurung, P., & Tuthill, J. C. (2018). Neural Coding of Leg Proprioception in Drosophila. Neuron, 100(3), 636-650.e636. doi:

Marques, T., Summers, M. T., Fioreze, G., Fridman, M., Dias, R. F., Feller, M. B., & Petreanu, L. (2018). A Role for Mouse Primary Visual Cortex in Motion Perception. Current Biology, 28(11), 1703-1713.e1706. doi:

Mateo, C., Knutsen, P. M., Tsai, P. S., Shih, A. Y., & Kleinfeld, D. (2017). Entrainment of Arteriole Vasomotor Fluctuations by Neural Activity Is a Basis of Blood-Oxygenation-Level-Dependent “Resting-State” Connectivity. Neuron, 96(4), 936-948.e933. doi:

Mayrhofer, J. M., El-Boustani, S., Foustoukos, G., Auffret, M., Tamura, K., & Petersen, C. C. H. (2019). Distinct Contributions of Whisker Sensory Cortex and Tongue-Jaw Motor Cortex in a Goal-Directed Sensorimotor Transformation. Neuron, 103(6), 1034-1043.e1035. doi:

Meier, M., & Borst, A. (2019). Extreme Compartmentalization in a Drosophila Amacrine Cell. Current Biology, 29(9), 1545-1550.e1542. doi:

Meshulam, L., Gauthier, J. L., Brody, C. D., Tank, D. W., & Bialek, W. (2017). Collective Behavior of Place and Non-place Neurons in the Hippocampal Network. Neuron, 96(5), 1178-1191.e1174. doi:

Mikael, T. E., David, R., Nancy, H.-D., Marco, W., Christoph, H., Rainer, A. L., . . . Marco, A. (2020). Surgical microscope with integrated fluorescence lifetime imaging for 5-aminolevulinic acid fluorescence-guided neurosurgery. Journal of Biomedical Optics, 25(7), 1-7. doi: 10.1117/1.jbo.25.7.071202.

Minamisawa, G., Kwon, S. E., Chevée, M., Brown, S. P., & O’Connor, D. H. (2018). A Non-canonical Feedback Circuit for Rapid Interactions between Somatosensory Cortices. Cell Reports, 23(9), 2718-2731.e2716. doi:

Minderer, M., Brown, K. D., & Harvey, C. D. (2019). The Spatial Structure of Neural Encoding in Mouse Posterior Cortex during Navigation. Neuron, 102(1), 232-248.e211. doi:

Mishra, A., Salari, A., Berigan, B. R., Miguel, K. C., Amirshenava, M., Robinson, A., . . . Zars, T. (2018). The Drosophila Gr28bD product is a non-specific cation channel that can be used as a novel thermogenetic tool. Scientific Reports, 8(1), 901. doi: 10.1038/s41598-017-19065-4.

Mitani, A., Dong, M., & Komiyama, T. (2018). Brain-Computer Interface with Inhibitory Neurons Reveals Subtype-Specific Strategies. Current Biology, 28(1), 77-83.e74. doi:

Mitani, A., & Komiyama, T. (2018). Real-Time Processing of Two-Photon Calcium Imaging Data Including Lateral Motion Artifact Correction. [Methods]. Frontiers in Neuroinformatics, 12(98). doi: 10.3389/fninf.2018.00098.

Moore, A. K., Weible, A. P., Balmer, T. S., Trussell, L. O., & Wehr, M. (2018). Rapid Rebalancing of Excitation and Inhibition by Cortical Circuitry. Neuron, 97(6), 1341-1355.e1346. doi:

Morcos, A. S., & Harvey, C. D. (2016). History-dependent variability in population dynamics during evidence accumulation in cortex. Nature Neuroscience, 19(12), 1672-1681. doi: 10.1038/nn.4403.

Moura, C. C., Bourdakos, K. N., Tare, R. S., Oreffo, R. O. C., & Mahajan, S. (2019). Live-imaging of Bioengineered Cartilage Tissue using Multimodal Non-linear Molecular Imaging. Scientific Reports, 9(1), 5561. doi: 10.1038/s41598-019-41466-w.

Murphy-Royal, C., Johnston, A. D., Boyce, A. K. J., Diaz-Castro, B., Institoris, A., Peringod, G., . . . Gordon, G. R. (2020). Stress gates an astrocytic energy reservoir to impair synaptic plasticity. Nature Communications, 11(1), 2014. doi: 10.1038/s41467-020-15778-9.

Oda, K., Vierock, J., Oishi, S., Rodriguez-Rozada, S., Taniguchi, R., Yamashita, K., . . . Nureki, O. (2018). Crystal structure of the red light-activated channelrhodopsin Chrimson. Nature Communications, 9(1), 3949. doi: 10.1038/s41467-018-06421-9.

Oppermann, J., Fischer, P., Silapetere, A., Liepe, B., Rodriguez-Rozada, S., Flores-Uribe, J., . . . Wietek, J. (2019). MerMAIDs: a family of metagenomically discovered marine anion-conducting and intensely desensitizing channelrhodopsins. Nature Communications, 10(1), 3315. doi: 10.1038/s41467-019-11322-6.

Orlova, N., Tsyboulski, D., Najafi, F., Seid, S., Kivikas, S., Kato, I., . . . Saggau, P. (2020). Multiplane Mesoscope reveals distinct cortical interactions following expectation violations. bioRxiv, 2020.2010.2006.328294. doi: 10.1101/2020.10.06.328294.

Parker, J. G., Marshall, J. D., Ahanonu, B., Wu, Y.-W., Kim, T. H., Grewe, B. F., . . . Schnitzer, M. J. (2018). Diametric neural ensemble dynamics in parkinsonian and dyskinetic states. Nature, 557(7704), 177-182. doi: 10.1038/s41586-018-0090-6.

Pearre, B. W., Michas, C., Tsang, J.-M., Gardner, T. J., & Otchy, T. M. (2019). Fast micron-scale 3D printing with a resonant-scanning two-photon microscope. Additive Manufacturing, 30, 100887. doi:

Peron, S., Pancholi, R., Voelcker, B., Wittenbach, J. D., Ólafsdóttir, H. F., Freeman, J., & Svoboda, K. (2020). Recurrent interactions in local cortical circuits. Nature, 579(7798), 256-259. doi: 10.1038/s41586-020-2062-x.

Pichler, P., & Lagnado, L. (2019). The Transfer Characteristics of Hair Cells Encoding Mechanical Stimuli in the Lateral Line of Zebrafish. The Journal of Neuroscience, 39(1), 112. doi: 10.1523/jneurosci.1472-18.2018.

Pisanello, M., Pisano, F., Hyun, M., Maglie, E., Balena, A., De Vittorio, M., . . . Pisanello, F. (2019). The Three-Dimensional Signal Collection Field for Fiber Photometry in Brain Tissue. [Original Research]. Frontiers in Neuroscience, 13(82). doi: 10.3389/fnins.2019.00082.

Pisano, F., Pisanello, M., Maglie, E., Balena, A., Sileo, L., Spagnolo, B., . . . Pisanello, F. (2018). Multipoint and large volume fiber photometry with a single tapered optical fiber implant. bioRxiv, 455766. doi: 10.1101/455766.

Podgorski, K., & Ranganathan, G. (2016). Brain heating induced by near-infrared lasers during multiphoton microscopy. Journal of Neurophysiology, 116(3), 1012-1023. doi: 10.1152/jn.00275.2016.

Poleg-Polsky, A., Ding, H., & Diamond, J. S. (2018). Functional Compartmentalization within Starburst Amacrine Cell Dendrites in the Retina. Cell Reports, 22(11), 2898-2908. doi:

Pottackal, J., Singer, J. H., & Demb, J. B. (2020). Receptoral Mechanisms for Fast Cholinergic Transmission in Direction-Selective Retinal Circuitry. Frontiers in cellular neuroscience, 14, 604163-604163. doi: 10.3389/fncel.2020.604163.

Pujala, A., & Koyama, M. (2019). Chronology-based architecture of descending circuits that underlie the development of locomotor repertoire after birth. eLife, 8, e42135. doi: 10.7554/eLife.42135.

Ramachandra, V., Pawlak, V., Wallace, D. J., & Kerr, J. N. D. (2020). Impact of visual callosal pathway is dependent upon ipsilateral thalamus. Nature Communications, 11(1), 1889. doi: 10.1038/s41467-020-15672-4.

Reinhard, K., Li, C., Do, Q., Burke, E. G., Heynderickx, S., & Farrow, K. (2019). A projection specific logic to sampling visual inputs in mouse superior colliculus. eLife, 8, e50697. doi: 10.7554/eLife.50697.

Ruiz-Uribe, N. E., Ahn, S. J., & Schaffer, C. B. (2019, 2019/04/14). Label Free Imaging of Cortical Blood Vessels Using Third Harmonic Generation (THG) Microscopy. Paper presented at the Biophotonics Congress: Optics in the Life Sciences Congress 2019 (BODA,BRAIN,NTM,OMA,OMP), Tucson, Arizona.

Samonds, J. M., Feese, B. D., Lee, T. S., & Kuhlman, S. J. (2017). Nonuniform surround suppression of visual responses in mouse V1. Journal of Neurophysiology, 118(6), 3282-3292. doi: 10.1152/jn.00172.2017.

Schiavo, J. K., Valtcheva, S., Bair-Marshall, C., Song, S. C., Martin, K. A., & Froemke, R. C. (2020). Innate sensitivity and plastic mechanisms in auditory cortex for reliable maternal behavior. bioRxiv, 2020.2003.2011.987941. doi: 10.1101/2020.03.11.987941.

Schiavo, J. K., Valtcheva, S., Bair-Marshall, C. J., Song, S. C., Martin, K. A., & Froemke, R. C. (2020). Innate and plastic mechanisms for maternal behaviour in auditory cortex. Nature, 587(7834), 426-431. doi: 10.1038/s41586-020-2807-6.

Scholl, B., Thomas, C. I., Ryan, M. A., Kamasawa, N., & Fitzpatrick, D. (2021). Cortical response selectivity derives from strength in numbers of synapses. Nature, 590(7844), 111-114. doi: 10.1038/s41586-020-03044-3.

Scholl, B., Wilson, D. E., & Fitzpatrick, D. (2017). Local Order within Global Disorder: Synaptic Architecture of Visual Space. Neuron, 96(5), 1127-1138.e1124. doi:

Scholl, B., Wilson, D. E., Jaepel, J., & Fitzpatrick, D. (2019). Functional Logic of Layer 2/3 Inhibitory Connectivity in the Ferret Visual Cortex. Neuron, 104(3), 451-457.e453. doi:

Scott, B. B., Constantinople, C. M., Akrami, A., Hanks, T. D., Brody, C. D., & Tank, D. W. (2017). Fronto-parietal Cortical Circuits Encode Accumulated Evidence with a Diversity of Timescales. Neuron, 95(2), 385-398.e385. doi:

Shen, J., Blute, T. A., Liberti, W. A., Yen, W., Liberti, D. C., Kotten, D. N., . . . Gardner, T. J. (2017). Songbird organotypic culture as an <em>in vitro</em> model for interrogating sparse sequencing networks. bioRxiv, 164228. doi: 10.1101/164228.

Smith, G. B., & Fitzpatrick, D. (2016). Viral Injection and Cranial Window Implantation for In Vivo Two-Photon Imaging. In S. D. Schwartzbach, O. Skalli & T. Schikorski (Eds.), High-Resolution Imaging of Cellular Proteins: Methods and Protocols (pp. 171-185). New York, NY: Springer New York.

Srinivasan, R., Huang, B. S., Venugopal, S., Johnston, A. D., Chai, H., Zeng, H., . . . Khakh, B. S. (2015). Ca2+ signaling in astrocytes from Ip3r2−/− mice in brain slices and during startle responses in vivo. Nature Neuroscience, 18(5), 708-717. doi: 10.1038/nn.4001.

Stein, I. S., Hill, T. C., Oh, W. C., Parajuli, L. K., & Zito, K. (2019). Two-Photon Glutamate Uncaging to Study Structural and Functional Plasticity of Dendritic Spines. In E. Hartveit (Ed.), Multiphoton Microscopy (pp. 65-85). New York, NY: Springer New York.

Takahashi, N., Moberg, S., Zolnik, T. A., Catanese, J., Sachdev, R. N. S., Larkum, M. E., & Jaeger, D. (2021). Thalamic input to motor cortex facilitates goal-directed action initiation. Current Biology. doi:

Takasaki, K., Abbasi-Asl, R., & Waters, J. (2020). Superficial Bound of the Depth Limit of Two-Photon Imaging in Mouse Brain. eNeuro, 7(1), ENEURO.0255-0219.2019. doi: 10.1523/eneuro.0255-19.2019.

Tan, H. L., Roth, R. H., Graves, A. R., Cudmore, R. H., & Huganir, R. L. (2020). Lamina-specific AMPA receptor dynamics following visual deprivation in vivo. eLife, 9, e52420. doi: 10.7554/eLife.52420.

Tang, A. D., Bennett, W., Bindoff, A. D., Collins, J., Garry, M. I., Summers, J. J., . . . Canty, A. J. (2021). Low intensity repetitive transcranial magnetic stimulation drives structural synaptic plasticity in the young and aged motor cortex. bioRxiv, 2021.2003.2010.434706. doi: 10.1101/2021.03.10.434706.

Thomas, C. I., Ryan, M. A., Scholl, B., Guerrero-Given, D., Fitzpatrick, D., & Kamasawa, N. (2021). Targeting Functionally Characterized Synaptic Architecture Using Inherent Fiducials and 3D Correlative Microscopy. Microscopy and Microanalysis, 27(1), 156-169. doi: Doi: 10.1017/s1431927620024757.

Tiriac, A., Smith, B. E., & Feller, M. B. (2018). Light Prior to Eye Opening Promotes Retinal Waves and Eye-Specific Segregation. Neuron, 100(5), 1059-1065.e1054. doi:

Tran, C. H. T., Peringod, G., & Gordon, G. R. (2018). Astrocytes Integrate Behavioral State and Vascular Signals during Functional Hyperemia. Neuron, 100(5), 1133-1148.e1133. doi:

Tran-Van-Minh, A., Rebola, N., Hoehne, A., & DiGregorio, D. A. (2019). Two-Photon Neurotransmitter Uncaging for the Study of Dendritic Integration. In E. Hartveit (Ed.), Multiphoton Microscopy (pp. 33-64). New York, NY: Springer New York.

Tsutsumi, S., Chadney, O., Yiu, T.-L., Bäumler, E., Faraggiana, L., Beau, M., & Häusser, M. (2020). Purkinje Cell Activity Determines the Timing of Sensory-Evoked Motor Initiation. Cell Reports, 33(12), 108537. doi:

Tsutsumi, S., Hidaka, N., Isomura, Y., Matsuzaki, M., Sakimura, K., Kano, M., & Kitamura, K. (2019). Modular organization of cerebellar climbing fiber inputs during goal-directed behavior. eLife, 8, e47021. doi: 10.7554/eLife.47021.

Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., . . . Margrie, T. W. (2021). A deep learning algorithm for 3D cell detection in whole mouse brain image datasets. PLOS Computational Biology, 17(5), e1009074. doi: 10.1371/journal.pcbi.1009074.

Vavladeli, A., Daigle, T., Zeng, H., Crochet, S., & Petersen, C. C. H. (2020). Projection-specific Activity of Layer 2/3 Neurons Imaged in Mouse Primary Somatosensory Barrel Cortex During a Whisker Detection Task. Function, 1(zqaa008). doi: 10.1093/function/zqaa008.

Wagner, M. J., Kim, T. H., Kadmon, J., Nguyen, N. D., Ganguli, S., Schnitzer, M. J., & Luo, L. (2019). Shared Cortex-Cerebellum Dynamics in the Execution and Learning of a Motor Task. Cell, 177(3), 669-682.e624. doi:

Wagner, M. J., Kim, T. H., Savall, J., Schnitzer, M. J., & Luo, L. (2017). Cerebellar granule cells encode the expectation of reward. Nature, 544(7648), 96-100. doi: 10.1038/nature21726.

Wang, C.-C., Moorhouse, S., Stain, C., Seymour, M., Green, E., Penfield, S., & Moger, J. (2018). In situ chemically specific mapping of agrochemical seed coatings using stimulated Raman scattering microscopy. []. Journal of Biophotonics, 11(11), e201800108. doi:

Wang, K., Du, Y., Liu, H., Gan, M., Tong, S., Wen, W., . . . Qiu, P. (2019). Visualizing the “sandwich” structure of osteocytes in their native environment deep in bone in vivo. []. Journal of Biophotonics, 12(4), e201800360. doi:

Wang, K., Pan, Y., Tong, S., Chen, X., Lu, Y., & Qiu, P. (2021). Deep-skin multiphoton microscopy in vivo excited at 1600 nm: A comparative investigation with silicone oil and deuterium dioxide immersion. []. Journal of Biophotonics, n/a(n/a), e202100076. doi:

Wang, K., Wen, W., Liu, H., Du, Y., Zhuang, Z., & Qiu, P. (2018). Transmittance Characterization of Objective Lenses Covering all Four Near Infrared Optical Windows and its Application to Three-Photon Microscopy Excited at 1820 nm. IEEE Photonics Journal, 10(3), 1-7. doi: 10.1109/jphot.2018.2828435. 

Wang, K., Wen, W., Wang, Y., Wang, K., He, J., Wang, J., . . . Qiu, P. (2017). Order-of-magnitude multiphoton signal enhancement based on characterization of absorption spectra of immersion oils at the 1700-nm window. Optics Express, 25(6), 5909-5916. doi: 10.1364/oe.25.005909.

Wang, Y., Wang, K., Wen, W., & Qiu, P. (2016). Comparison of Signal Detection of GaAsP and GaAs PMTs for Multiphoton Microscopy at the 1700-nm window. IEEE Photonics Journal, 8(3), 1-6. doi: 10.1109/jphot.2016.2570005. 

Weisenburger, S., Tejera, F., Demas, J., Chen, B., Manley, J., Sparks, F. T., . . . Vaziri, A. (2019). Volumetric Ca2+ Imaging in the Mouse Brain Using Hybrid Multiplexed Sculpted Light Microscopy. Cell, 177(4), 1050-1066.e1014. doi:

Wilson, D. E., Scholl, B., & Fitzpatrick, D. (2018). Differential tuning of excitation and inhibition shapes direction selectivity in ferret visual cortex. Nature, 560(7716), 97-101. doi: 10.1038/s41586-018-0354-1.

Wilson, D. E., Smith, G. B., Jacob, A. L., Walker, T., Dimidschstein, J., Fishell, G., & Fitzpatrick, D. (2017). GABAergic Neurons in Ferret Visual Cortex Participate in Functionally Specific Networks. Neuron, 93(5), 1058-1065.e1054. doi:

Wilson, D. E., Whitney, D. E., Scholl, B., & Fitzpatrick, D. (2016). Orientation selectivity and the functional clustering of synaptic inputs in primary visual cortex. Nature Neuroscience, 19(8), 1003-1009. doi: 10.1038/nn.4323.

Xin, Y., Zhong, L., Zhang, Y., Zhou, T., Pan, J., & Xu, N.-l. (2019). Sensory-to-Category Transformation via Dynamic Reorganization of Ensemble Structures in Mouse Auditory Cortex. Neuron, 103(5), 909-921.e906. doi:

Yao, S., Yuan, P., Ouellette, B., Zhou, T., Mortrud, M., Balaram, P., . . . Cetin, A. (2020). RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations. Nature Methods, 17(4), 422-429. doi: 10.1038/s41592-020-0774-3.

Yap, K., Drakew, A., Smilovic, D., Rietsche, M., Paul, M. H., Vuksic, M., . . . Deller, T. (2020). The actin-modulating protein synaptopodin mediates long-term survival of dendritic spines. eLife, 9, e62944. doi: 10.7554/eLife.62944.

Ye, L., Orynbayev, M., Zhu, X., Lim, E. Y., Dereddi, R. R., Agarwal, A., . . . Paukert, M. (2020). Ethanol abolishes vigilance-dependent astroglia network activation in mice by inhibiting norepinephrine release. Nature Communications, 11(1), 6157. doi: 10.1038/s41467-020-19475-5.

Yu, C.-H., Stirman, J. N., Yu, Y., Hira, R., & Smith, S. L. (2020). Diesel2p mesoscope with dual independent scan engines for flexible capture of dynamics in distributed neural circuitry. bioRxiv, 2020.2009.2020.305508. doi: 10.1101/2020.09.20.305508.

Yuhao, Y., Niraj, S., & Fake, L. (2020). Monitoring uptake of palmitic acid by glioma cells using stimulated Raman scattering microscopy. Paper presented at the Proc.SPIE.

Zeiger, W. A., Marosi, M., Saggi, S., Noble, N., Samad, I., & Portera-Cailliau, C. (2020). Plasticity after cortical stroke involves potentiating responses of pre-existing circuits but not functional remapping to new circuits. bioRxiv, 2020.2011.2009.375840. doi: 10.1101/2020.11.09.375840.

Zeiger, W. A., Marosi, M., Saggi, S., Noble, N., Samad, I., & Portera-Cailliau, C. (2021). Barrel cortex plasticity after photothrombotic stroke involves potentiating responses of pre-existing circuits but not functional remapping to new circuits. Nature Communications, 12(1), 3972. doi: 10.1038/s41467-021-24211-8.

Zhao, L., Li, Z., Vong, J. S. L., Chen, X., Lai, H.-M., Yan, L. Y. C., . . . Ko, H. (2020). Pharmacologically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain. Nature Communications, 11(1), 4413. doi: 10.1038/s41467-020-18249-3.

Zhao, Y., Bushey, D., Zhao, Y., Schreiter, E. R., Harrison, D. J., Wong, A. M., & Campbell, R. E. (2018). Inverse-response Ca2+ indicators for optogenetic visualization of neuronal inhibition. Scientific Reports, 8(1), 11758. doi: 10.1038/s41598-018-30080-x.

Zhou, L., Nho, K., Haddad, M. G., Cherepacha, N., Tubeleviciute-Aydin, A., Tsai, A. P., . . . LeBlanc, A. C. (2021). Rare CASP6N73T variant associated with hippocampal volume exhibits decreased proteolytic activity, synaptic transmission defect, and neurodegeneration. Scientific Reports, 11(1), 12695. doi: 10.1038/s41598-021-91367-0.

Zhu, Y., & Gabbiani, F. (2016). Fine and distributed subcellular retinotopy of excitatory inputs to the dendritic tree of a collision-detecting neuron. Journal of Neurophysiology, 115(6), 3101-3112. doi: 10.1152/jn.00044.2016.

Zhu, Y., & Gabbiani, F. (2018). Combined Two-Photon Calcium Imaging and Single-Ommatidium Visual Stimulation to Study Fine-Scale Retinotopy in Insects. In R. V. Sillitoe (Ed.), Extracellular Recording Approaches (pp. 185-206). New York, NY: Springer New York.


Download our product sheet here.

Compare ScanImage Versions

Feature Description

ScanImage BASIC


Resonant-Galvo and Galvo-Galvo Frame Scanning
Synchronization to laser clock (vDAQ)
Beam control and selective power delivery via power boxes
Volume acquisition with motorized stages or fast-focusing devices (ETL, Piezo, etc)
Scriptability in Matlab, extensibility via user functions
Big Tiff file creation
FastZ-actuator tuning & Independent Z-control for multiple scanners
Live histogram for imaging channels
Custom power depth adjustment profiles
Integration with the electrophysiology package WaveSurfer
Offline data viewer, Online 3D Motion Correction & Oscilloscope Mode for Noise Analysis
Live motor position update in GUI (for selected stages)
New resource architecture with device widgets
Beam modulation with motorized half-wave plates
Support for vDAQ & high-speed vDAQ
Actively developed and maintained & includes one year of technical support
Custom waveform generator (vDAQ only)
Ancillary signal recorder(vDAQ only)
MCM-6000 redbox support
Galil DMC-4040 stage support
Low rep-rate laser support
Polygonal scanner support
Synchronization with PicoQuant FLIM Systems
Multiple region of interest (mROI) scanning
Online analysis (ROI Integration)
Perspective alignment between multiple scanner
Alignment of scanners and stage
Simultaneous imaging and photo stimulation
Arbitrary line scanning using two galvos
Command waveform optimization
Support for 2P mesoscope & 3- photon imaging
SLM support for targeted photostimulation
Acquistion gating for low rep rate Lasers
Camera support for widefield alignment
SLM diffraction efficiency calibration
ScanImage remote control
Tiling Tool for mosaic imaging and FOV relocation
3D Shot holographic targeting workflow
Support for Scientifica HoloStim-3D

Who Is Using ScanImage?

ScanImage is used across the globe by the most prestigious laboratories. 

Cited in Peer Reviewed Scientific Publications

ScanImage’s utility is underscored by the number of references it receives in the worlds most important scientific publications. See examples below: 

Frequently Asked Questions (FAQ)

Which microscopes can ScanImage control?

ScanImage can control custom built and commercial microscopes from Scientifica, Sutter Instruments, Prospective Instruments and Thorlabs. ScanImage uses the powerful vDAQ data acquisition hardware to control all aspects of the microscope. For legacy systems, data acquisition systems from National Instruments are also supported.

Is ScanImage customizable?

ScanImage is written in Matlab and is source accessible. ScanImage is fully scriptable and automatable in Matlab, and is extensible through user functions. Our expert engineers are also available to perform custom software development as a service.

Which microscope hardware does ScanImage control?

ScanImage supports numerous devices, including: resonant and linear scanners, galvos, beam modulators, motor controllers, fast focus, shutters, cameras, and spatial light modulators. A complete list of supported microscope hardware can be found in the ScanImage documentation

Does ScanImage require a Matlab license?

ScanImage requires Matlab 2017a or later. A Matlab license needs to be obtained separately.

Does ScanImage support the Mini2P?

The Mini2P was designed for use with ScanImage software and the vDAQ data acquisition card. Weighing <3g, the Mini2P enables 2-photon microscopy of freely moving mice. It can image hundreds of neurons in a volume, with temporal resolution suitable for GCaMP6-labeled mice.


For more information, see the research article that introduces the Mini2P, Large-scale two-photon calcium imaging in freely moving mice and the Technology Feature on the Mini2P in NatureThumb-sized microscope captures images deep inside the brains of active animals.


To use the Mini2P with ScanImage, see the build protocol and software installation documents included in the MINI2P toolbox GitHub repository.

Does ScanImage support 3P microscopy?

ScanImage offers tools to optimize the SNR for 3P acquisitions. Since 3P lasers typically have a lower repetition rate, ScanImage can mask out the noise signal between laser pulses.

How does ScanImage integrate with my experiment?

ScanImage offers powerful triggering schemes that allow to precisely align the image acquisition with a behavioral experiment.

What is the maximum acquisition speed that ScanImage supports and the maximum duration of an image acquisition?

ScanImage supports resonant scanners with line rates of up to 100kHz. The vDAQ acquires data with a sample rate of up to 125MHz. The high speed add-on for the vDAQ acquires data with up to 2.7GHz. vDAQ allows synchronizing the digital data conversion to the laser to enable techniques such as time correlated photon counting and time multiplexed acquisition.

ScanImage supports acquisitions of arbitrary durations. The only practical limit to the acquisition length is the size of the hard drive.



Robust Professional Support

Our service sets us apart, with a team that includes Ph.D. neuroscientists, experts in microscopy, stereology, neuron reconstruction, and image processing.  We’ve also developed a host of additional support services, including:

  • Forums
    We have over 25 active forums where open discussions take place.
    >> Learn More
  • On-Site/Training
    We’ve conducted over 750 remote software installations.
    >> Learn More
  • Webinars
    We’ve created over 55 webinars that demonstrate our products & their uses.
    >> Learn More

Request an Expert Demonstration

We offer both a free demonstration and a free trial copy of ScanImage. During your demonstration you’ll also have the opportunity to talk to us about your hardware, software, or experimental design questions with our team of Ph.D. neuroscientists and experts in microscopy, neuron tracing, and image processing.

Related Products

RMR Scanner®

Fast and flexible 2P imaging. Powered by ScanImage.




Vidrio’s Data Acquisition Card is a next generation all in one controller for your microscope. It controls Galvos, Pockels Cells, Fast Z devices, shutters and much more.


A revolutionary new microscope based on a technological breakthrough called Scanned Line Angular Projection (SLAP) two photon laser scanning microscopy.


Ground-breaking light sheet microscope system for cleared specimens.