ScanImage protocols

ScanImage statistics

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Associated diseases

Associated diseases

ScanImage specifications


Unique identifier OMICS_06507
Name ScanImage
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for ScanImage

ScanImage in pipeline

PMCID: 5005324
PMID: 27630827
DOI: 10.3389/fcimb.2016.00090

[…] by two-photon microscopy with the ti:sapphire laser (mira, coherent) intensity at 60 mw and input wavelength of 850 nm. laser scanning images were collected at 0.5−1 μm incremental depths using scanimage (janelia farms, hhmi). images were saved in a single tiff file with 16 bit depth. deconvolution of the images was performed using autoquant × 3 and 3d models of z-stacks were generated […]

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ScanImage in publications

PMCID: 5947940
PMID: 29706545
DOI: 10.1016/j.cell.2018.03.075

[…] were passed through a high-speed amplifier (hca-4m-500k-c, laser components) and a custom-designed integrator circuit to maximize the signal-to-noise ratio (). the microscope was controlled through scanimage (vidrio technologies) via a pci-6110 daq board (national instruments). images were acquired at a resolution of 256 × 256 pixels and a frame rate of 5 hz. all experiments were carried […]

PMCID: 5946730
PMID: 29656873
DOI: 10.1016/j.neuron.2018.03.037

[…] necessary., experiments were performed 16-34 days after virus injection (p54-110). we used a commercial two-photon microscope with a resonant-galvo scanhead (b-scope, thorlabs, ely uk) controlled by scanimage 4.2 (), with an acquisition frame rate of about 30hz (at 512 by 512 pixels, corresponding to a rate of 4-6 hz per plane), which was later interpolated to a frequency of 10 hz, common […]

PMCID: 5894120
PMID: 29562189
DOI: 10.1016/j.celrep.2018.02.081

[…] a 580-nm long-pass dichroic mirror followed by a 525/50-nm bandpass filter (semrock) and collected by a gaasp photomultiplier tube (hamamatsu). microscope control and data acquisition was managed by scanimage 2015 (vidrio technologies). images were acquired at 30 hz with a resolution of 512 × 512 pixels., animals were perfused after imaging, and their brains were subsequently sliced. tissue […]

PMCID: 5864847
PMID: 29615867
DOI: 10.3389/fnmol.2018.00083

[…] anesthesia (1%–1.5%) with a custom-built two-photon microscope, using a ti:sapphire laser (chameleon ultra ii; coherent inc.) tuned to 910 nm, a 40× 0.8 na water immersion objective (olympus), and scanimage 3.8 software (rrid:scr_014307; pologruto et al., ) written in matlab (mathworks; rrid:scr_001622). mice were secured to the microscope using the titanium head bar. guided by the maps […]

PMCID: 5877421
PMID: 29539419
DOI: 10.1016/j.celrep.2018.02.064

[…] with fluorescent dye; recording commenced following a ~30-min interval to allow the dye to fill the dendrites., two-photon imaging was performed using a microscope (sutter instruments) controlled by scanimage (vidrio technologies) and equipped with a 20×/0.95 na objective (olympus) and photomultiplier tubes filtered to detect green (500-540 nm) and red (575-640 nm) fluorescence excited by 920-nm […]

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ScanImage institution(s)
Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

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