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NeuroDeep - the minimally invasive in vivo Microendoscope

Structural and functional imaging in deep tissue. Microendoscopy through a single fibre endoscope.

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Advantages of Microendoscopy

Minimal tissue damage

Insertion of our unique single-fibre probe has minimal effect on surrounding tissue and minimal effect on the physiological brain function.

Subcellular resolution

Our technology enables single cell imaging and imaging of subcellular structures like axons, dendritic spines or buttons for studies of neuronal plasticity and connectivity.

Probe path through the entire brain illuminated by florescent labelling.
Endomicroscopy DeepEn icon in vivo microscopy in the deepest brain

Deep tissue penetration

Our 100µm probe is stable enough to allow smooth insertion into deep and sensitive brain region that are currently not accessible with other technologies.

Probe path through the entire brain illuminated by florescent labelling.

NeuroDeep® Microendoscopy Platform 

Powerful bioimaging through a single fibre endoscope.

DeepEn’s unique NeuroDeep platform enables laser-scanning fluorescence imaging at the tip of a multimode fibre probe (⌀100μm) at any depth in living tissue with minimal structural damage and thus minimal effect on physiological function. Relying on advanced holographic technology, the device is capable of random-access observations across a 100 μm diameter field of view with submicrometric lateral resolution and on-the-fly adjustment of the focal distance. A read-out speed of up to 25,000 focal points per second allows for high-speed recording of neuronal activity. The instrument is a powerful tool for neuroscience, biomedical research and pharma laboratories.


High-Resolution Imaging

Achieves submicrometre resolution of 0.7 µm, adhering to the Abbe limit for probes with 0.37 NA, operating at a wavelength of 491 nm.

Reduced Probe Footprint

The probe’s thickness of only 110 µm minimizes tissue damage, allowing for direct, image-guided insertion and immediate imaging.

Adjustable Focal Distance

Allows imaging across a set of preselected focal distances ranging from 0 to 50 µm from the probe facet.

Structured Illumination

Incorporates patterned illumination of user-selected areas for enhancing data acquisition rate to a kilohertz level.

Random-Access Scanning

25,000 focal points per second for swift selective scanning with no delays, regardless of the relative distance between scanning regions.

Excitation Wavelengths

Offers the flexibility of using either 491 nm or 532 nm excitation wavelengths, catering to a broad range of labelling options. Other wavelengths are possible on demand.

Multicolour Detection

Features simultaneous recording and visualization of different spectrally-separated fluorophores, excitable at the working wavelength.

Field of View

The field of view is spanning 100 µm in diameter and thus allows for imaging of multiple neurons across the fibre facet.


1) Structural Imaging

Imaging modality with full resolution at slow frame rate. The user can choose a slower scanning rate to achieve the submicron resolution to image individual cells, or small structures like dendrites and spines or even sub-cellular compartments.

2) Functional (Ca2+) imaging

Imaging with fast frame rate at low spacial resolution. Users can switch to this imaging modality for recording neuronal activity. The required higher frame rate is achieved by decreasing the spacial resolution, focussing only on the selected readout areas.

3) Blood flow velocity tracking

Measuring blood flow velocity in individual blood vessels for application in stroke research. Traces of individual red blood cells can be imaged (vasculature stained with FITC-dextran).

Source: Stibůrek, M., Ondráčková, P., Tučková, T. et al. 110 μm thin endo-microscope for deep-brain in vivo observations of neuronal connectivity, activity and blood flow dynamics. Nat Commun 14, 1897 (2023).

Discover with microendoscopy what has never been seen.

Real-time recording of active neuron structures during insertion of a NeuroDeep probe, visible on the user interface.

  • Study in anaesthetised mouse model (Thy1-GFP line).
  • Depth 5 mm – level of the amygdala
  • Field of view: approx. 100×100 μm

Neuroscientific Background

In-vivo imaging through single Fibres

Holographic endoscope technology is an impactful innovation from the field of Neurophotonics. It is based on years of rigorous research conducted at renowned institutes, and was validated for deep-brain imaging in multiple independent laboratories.

Holographic Microendoscopy

This innovative technology turns a single multimode optical fibre into a laser-scanning microscope with much less traumatic application in-vivo and superior imaging performance. 

The technology is based on precise control of light transport through optical fibres. During an initial calibration process, the complex light propagation through the fibre is characterised (transmission matrix „TM“ of the fibre) to achieve a focal point at the distal end of the fibre. The focal point scans over the sample, inducing emission of fluorescent light, which is collected back through the fibre and used to generate a microscopic image.





Endomicroscopy_fibre-based endocopy for deep brain in vivo imaging


Endomicroscopy_subcellular spatial resolution for deep-brain imaging


Endomicroscopy_thin endomicroscope for deep-brain in vivo observations

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Our Mission

DeepEn provides laboratories with powerful tools to study the deepest regions of the brain. Our mission is to support researchers in discovering, developing and applying the tools for prevention, diagnosis, and treatment of brain disorders.

DeepEn is funded by the Federal Ministry for Economic Affairs and Climate Action and the European Social Fund as part of the EXIST program.

DeepEn is a research transfer spinoff from Leibniz-Institute of Photonic Technologies


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