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HelioScan specifications


Unique identifier OMICS_29561
Name HelioScan
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Output format TIFF+XML
Programming languages C++, MATLAB, Ruby
Computer skills Medium
Stability Stable
Maintained Yes




No version available



  • person_outline Fritjof Helmchen

Additional information


Publication for HelioScan

HelioScan citations


Sensory representation of an auditory cued tactile stimulus in the posterior parietal cortex of the mouse

Sci Rep
PMCID: 5958066
PMID: 29773806
DOI: 10.1038/s41598-018-25891-x

[…] We used a custom-built two-photon microscope controlled by HelioScan, equipped with a Ti:sapphire laser system (~100-fs laser pulses; Mai Tai HP; Newport Spectra Physics), a water-immersion objective (16 × LWDPF, 0.8 NA; Nikon), galvanometric scan mirrors (mo […]


An R CaMP1.07 reporter mouse for cell type specific expression of a sensitive red fluorescent calcium indicator

PLoS One
PMCID: 5480891
PMID: 28640817
DOI: 10.1371/journal.pone.0179460
call_split See protocol

[…] -written C++ software ‘SCOPE’ was used (Visual Studio C++; see http://rkscope.sourceforge.net/). For Figs , , and , a Sutter Instrument Movable Objective Microscope was used, which was controlled by HelioScan (Langer et al., 2013).For longitudinal assessment of stability, L2/3 neurons in S1 cortex were repeatedly imaged in head-restrained, awake mice starting at 1 DPI, and up to 100 DPI (in some […]


Stimulus relevance modulates contrast adaptation in visual cortex

PMCID: 5298877
PMID: 28130922
DOI: 10.7554/eLife.21589.012
call_split See protocol

[…] For the experiments on mice not engaged in visually-guided behavior, fluorescence was measured with a custom-built two-photon microscope controlled by HelioScan (www.helioscan.org) (). The scanhead was based on an 8 kHz resonant scanner (Cambridge Technology, Switzerland), used in bidirectional mode. Images were acquired at 77.7 Hz with a resolution […]


Dendritic NMDA spikes are necessary for timing dependent associative LTP in CA3 pyramidal cells

Nat Commun
PMCID: 5116082
PMID: 27848967
DOI: 10.1038/ncomms13480
call_split See protocol

[…] 10 and 15 mW. Fluorescence was detected using two photomultiplier tubes using 525/50 nm (green channel) and 620/60 nm (red channel) emission filters. Scanning and image acquisition were controlled by HelioScan software. Time series of Fluo-5F fluorescence images were acquired at 10 Hz with 100 × 100 pixel resolution across imaging fields encompassing neuronal dendrites. The dimensions of a field o […]


Long range population dynamics of anatomically defined neocortical networks

PMCID: 4929001
PMID: 27218452
DOI: 10.7554/eLife.14679.024
call_split See protocol

[…] For in vivo identification of LSSmKate-positive feedforward and tdTomato-positive feedback neurons, 3D-volume image stacks were taken on a standard custom-built 2-photon microscope controlled by HelioScan34, equipped with a Ti:sapphire laser system (~100-fs laser pulses; Mai Tai HP; Newport Spectra Physics), a water-immersion objective (40×LUMPlanFl/IR, 0.8 NA; Olympus), galvanometric scan mi […]


FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two photon calcium neuronal imaging data

Front Neuroinform
PMCID: 4299654
PMID: 25653614
DOI: 10.3389/fninf.2014.00085

[…] FocusStack already provides in-build access to the data format of a previously published 3D imaging software, “Focus” (Göbel et al., ) and the open source project “HelioScan” (Langer et al., ). There are presently a plethora of binary data formats in which two-photon imaging systems store recorded calcium signals. Many of these are ad-hoc, “in-house” formats, an […]


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HelioScan institution(s)
Brain Research Institute, University of Zurich, Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland; Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, Switzerland; Department of Neuroscience, Uppsala University, Uppsala, Sweden
HelioScan funding source(s)
Supported by a PhD fellowship from the Roche Research Foundation and grants from the Swiss National Science Foundation (SNSF; grants 310030-127091), the German-Swiss Research Group “Barrel Cortex Function” (FOR1341, SNSF 310030-130826), the EU-FP7 program (BRAIN-I-NETS project 243914), and the Swiss SystemsX.ch Initiative (project 2008/2011-Neurochoice).

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