fbpx Femtonics - Femto3D Atlas multiphoton microscope for neuroscience researches


In vivo high-speed 3D imaging of neuronal activity of more than 2000 neurons


Automatic broadband wavelength tuning between 750 - 1050 nm


Simultaneous 3D photostimulation and 3D imaging


In vivo 3D imaging with motion correction in behaving model animals

Breakthrough innovation in multiphoton microscopy

The Innovation Award winner FEMTO3D Atlas combines high-tech science and engineering in 3D measurements. It implements and goes beyond the traditional galvo and resonant scanner-based imaging functions and combines them with a unique fast 3D imaging feature, providing an All-in-one solution. The FEMTO3D Atlas enables its users to scan neuronal, dendritic, or other biological processes in 3D, up to a million times faster than classical scanning methods, at a preserved two-photon resolution.

Watch our webinar about the FEMTO3D Atlas multiphoton microscope.



Neural networks consist of thousands of neurons dispersed in 3D space, often across many cortical layers of the brain. 3D random-access scanning performed by AO technology is the best choice to reveal the dynamics of the neural networks while processing information. It enables you to record neuronal activity from cell populations consisting of up to thousands of cells in vivo. The 3D anti-motion technology combined with new scanning methods united in FEMTO3D Atlas provides a flexible solution to gather motion-corrected data in large volumes at high framerates during behavior

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3D random-access point scanning extended by drifting the focal point along scanning elements with various shapes and sizes allows imaging without interruption at multiple dendritic branches. The sampling is continuous during the drift, so this scanning mode gives more detailed spatial resolution without changing the overall scanning time which reminds as high as the point scanning.  As a result, function of thin dendritic segments or even spines, single action potentials can be revealed. See more Chiovini et. al, Neuron (2014).

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Our anti-motion technology enables cell activity to be captured while an animal is moving in virtual reality and performing tasks. To preserve signals, scanning points are extended to drifted lines which are precisely fitted to each other resulting in surface or volume elements enclosing the target object. These elements cover not only the pre-selected ROIs but also the neighboring areas giving an opportunity for motion correction by preserving all fluorescent information during motions and decreasing the artefacts by more than one order of magnitude in behaving animals.

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Photostimulation techniques allow activating cells in a selective and precise manner, which makes them advantageous for various biological applications, from studies of synaptic plasticity to experiments investigating learning and memory in vivo. To the FEMTO3D Atlas Dichro extension, a second laser can be coupled enabling users to perform optogenetic stimulation or uncaging with calcium imaging, simultaneously, even in different cell populations.

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Using the AO technology in combination with our easy-to-use data acquisition software package provides maximal flexibility in fast selection of 3D ROIs with various shapes and sizes such as points, trajectories, squares, etc. The preselected ROIs can be precisely and rapidly targeted without wasting measurement time on unnecessary background increasing further the measurement speed up to 30 kHz and the signal-to-noise ratio by several orders of magnitude in comparison to classical raster scanning.

The novel 3D scanning methods of the FEMTO3D Atlas microscope collect all fluorescence information from the regions of ROIs during 3D measurements in the brain of behaving, moving animals that are performing tasks in virtual reality. To preserve fluorescent signals during movement, scanning points are extended in 3D to planar or volume elements, always enclosing the target object (Szalay et al 2016, Neuron). A 10–1,000 Hz sampling rate, necessary to resolve neural activity at the individual ROIs, is maintained.  Therefore, our technology allows for in vivo motion artefact correction on a fine spatial scale.

The high-speed raster scan mode of Atlas provides a scanning speed of 40 fps at 510 x 510 pixels and 500 x 500 µm2, which is faster than most resonant scanning multiphoton microscopes, their highest speed being around 30 fps. Thanks to the AO technology, the scanning plane can be arbitrarily chosen while the speed is maintained: the fast-scanned plane can be perpendicular to the axis of the objective, or lying in an arbitrary angle in X and/or Y.

Using the 3D random-access excitation method of FEMTO3D Atlas Dichro, scanning methods of the Femtonics AO technology are available with flexible parameters for photostimulation. Depending on the selected scanning pattern, users can stimulate sparsely distributed individual cells or dendritic processes in a large volume with high precision. By rapidly switching between the two laser lines, activity can be recorded near-simultaneously with photostimulation.

The FEMTO3D Atlas can be combined with a preexisting upright microscope through its adjustable, modular frame. The variable frame of the ATLAS enables us to couple the scope to numerous host microscopes. Therefore, the Atlas can extend existing setups with a fast 3D functional imaging capability. In addition, Atlas can work as an individual system: our basic Femtonics 2P Platform scope has been developed exclusively for the FEMTO3D Atlas. The microscope has an integrated beam stabilization unit, which eliminates all kinds of optical errors generated by thermal drift, motion, the aging of the laser system, or any other perturbation next to the AO deflectors.


The novel features of the FEMTO3D Atlas are the electrically tunable acousto-optic deflectors (AODs) which are responsible for the X, Y, and Z focusing (acousto-optic or AO technology). These deflectors do not contain scanning mirrors or any other slowly moving mechanical components, so the positioning of the focal spot is fast, flexible, stable and independent of the travelling distance. This positioning freedom results an extremely high scanning speed, up to 30 kHz at any 3D location in a cubic millimeter volume under the objective.   


Demo rooms

Budapest, Hungary

Group Leader: Dr. Balázs Rózsa

Two-Photon Imaging Center

Institute of Experimental Medicine

Eötvös Loránd Research Network




New York, USA

Principal Investigator: Prof. Dr. Attila Losonczy

Losonczy Lab

Mortimer Zuckerman Mind Brain and Behavior Institute and the Kavli Institute for Brain Science

Columbia University




Jena, Germany

Group Leader: Prof. Dr. Knut Holthoff

BioImaging Group

Jena University Hospital




Basel, Switzerland

Group Leader: Dr. Botond Roska

Central Visual Circuits & Human Retinal Circuit Groups

Institute of Molecular and Clinical Ophthalmology Basel




New York, United States – Coming soon

Contact Researcher: Dr. Christopher Makinson

Institute for Genomic Medicine / Department of Neurology

Columbia University Irving Medical Center




Genova, Italy – Coming soon

Director, Principal Investigator: Prof. Dr. Fabio Benfenati

Neuroscience and Smart Materials

IIT Central Research Labs Genova





CLARITY analysis of the Cl/pH sensor expression in the brain of transgenic mice. Artem V.Diuba, Dmitry V.Samigullin, Attila Kaszas, Francesca Zonfrillo, Anton Malkov, Elena Petukhova, Antonio Casini, Daniele Arosio, Monique Esclapez, Cornelius T. Gross, Piotr Bregestovski, Neuroscience (2019)

Functional Synaptic Architecture of Callosal Inputs in Mouse Primary Visual Cortex. Kuo-Sheng Lee, Kaeli Vandemark, Dávid Mezey, Nicole Shultz, David Fitzpatrick, Neuron (2019)

Fast 3D Imaging of Spine, Dendritic, and Neuronal Assemblies in Behaving Animals. Gergely Szalay, Linda Judak, Gergely Katona, Katalin Ocsai, Gabor Juhasz, Mate Veress, Zoltan Szadai, Andras Feher, Tamas Tompa, Balazs Chiovini, Pal Maak, Balazs Rozsa, Neuron (2016)

Accurate spike estimation from noisy calcium signals for ultrafast three-dimensional imaging of large neuronal populations in vivo. Thomas Deneux, Attila Kaszas, Gergely Szalay, Gergely Katona, Tamas Lakner, Amiram Grinvald, Balazs Rozsa & Ivo Vanzetta, Nature Communications (2016)

Single-cell-initiated monosynaptic tracing reveals layer-specific cortical network modules. Wertz A, Trenholm S, Yonehara K, Hillier D, Raics Z, Leinweber M, Szalay G, Ghanem A, Keller G, Rozsa B, Conzelmann KK, Roska B, Science (2015)

Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes. Gergely Katona, Gergely Szalay, Pál Maak, Attila Kaszas, Mate Veress, Daniel Hillier, Balazs Chiovini, E Sylvester Vizi, Botond Roska & Balazs Rozsa, Nature Methods (2012)

Localized Neuron Stimulation with Organic Electrochemical Transistors on Delaminating Depth Probes. Williamson A, Ferro M, Leleux P, Ismailova E, Kaszas A, Doublet T, Quilichini P, Rivnay J, Rozsa B, Katona G, Bernard C, Malliaras GG., Advanced Materials (2015)

Dendritic spikes induce ripples in parvalbumin interneurons during hippocampal sharp waves. B Chiovini, G F Turi, G Katona, A Kaszas, D Palfi, P Maak, G Szalay, M F Szabo, Z Szadai, Sz Kali and B Rozsa, Neuron (2014)

Sensitization of neonatal rat lumbar motoneuron by the inflammatory pain mediator bradykinin. Mouloud Bouhadfane, Attila Kaszas, Balazs Razsa, Ronald M Harris-Warrick, Laurent Vinay, Frederic Brocard, eLife (2015)

Unitary GABAergic volume transmission from individual interneurons to astrocytes in the cerebral cortex. Rozsa M, Baka J, Borde S, Rozsa B, Katona G, Tamas G, Brain Struct Funct. (2017)