FARSIGHT statistics

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Citations per year

Citations chart

Popular tool citations

chevron_left Biological network reconstruction Cell tracking Spectral unmixing Image segmentation Neuron tracing Image segmentation Cell tracking 3D image analysis Neuron tracing Spectral images analysis Animal behavior tracking Image registration Biological network reconstruction Neuron tracing chevron_right
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Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases


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FARSIGHT specifications


Unique identifier OMICS_06484
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for FARSIGHT

FARSIGHT in pipeline

PMCID: 5134023
PMID: 28334699
DOI: 10.1098/rsif.2016.0725

[…] a technique originally developed to analyse fluid flow [], has also been employed to track cells in epithelial tissues []., software implementations and computational tools for cell tracking include farsight [] (segmentation only), seedwatersegmenter [] (nearest-neighbour tracking), ilastik [] (chain-graph models), tufts tissue tracker [] (min-cost max-flow algorithm), tracking with gaussian […]

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FARSIGHT in publications

PMCID: 5932171
PMID: 29755325
DOI: 10.3389/fnana.2018.00028

[…] the contours in a dense grid. however, these methods require excessive data fetches and current theory doesn't extend to higher-dimensional images., three-dimensional techniques are available in the farsight toolkit (bjornsson et al., ), and rely on a multi-step process that binarizes the input based on graph cuts and then detects the seed points using a scale-space log filter. various versions […]

PMCID: 5572162
PMID: 28844202
DOI: 10.1186/s12915-017-0407-1

[…] fluorescently labeled sperm were obtained using a zeiss lsm 880 microscope with a plan-apochromat 40×/1.4 oil differential interference contrast (dic) objective. image stacks were analyzed using the farsight nucleus editor (http://www.farsight-toolkit.org/wiki/nucleuseditor). we note that when the fluorescent marker was crossed to a daf-16 mutant background, it was not confined to the nuclei. […]

PMCID: 5660146
PMID: 28699046
DOI: 10.1007/s10456-017-9565-6

[…] the development and improvement of equipment such as multi-photon microscopes and light sheet microscopes. furthermore, numerous relevant software tools have been developed, including imagej, vaa3d, farsight, neuronstudio, amira, and imaris [–]., here, we employed optical clearance methods to study gbm cells in the mouse brain microenvironment. we demonstrate that optically cleared tissues […]

PMCID: 5334646
PMID: 28255161
DOI: 10.1038/srep43693

[…] segmentation by powerful methods from graph theory and computational topology., the cell nuclei segmentation is objective, robust and exceeds the performance of well-established programs such as farsight and cellprofiler. it is insensitive towards intensity variations and capable of separating apparently touching cell nuclei in regions of different cellular density. the initial local […]

PMCID: 5406431
PMID: 27696155
DOI: 10.1007/s00429-016-1316-8

[…] question and the resources that are available. on one hand, a thorough, tridimensional analysis of main and fine processes may require advanced computational skills and powerful hardware (e.g., farsight-based tools). on the other hand, commercially available tools are rather user-friendly, yet they are costly and time-consuming [e.g., neurolucida (mbf bioscience, usa), imaris (bitplane, […]

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FARSIGHT institution(s)
Center for Neural Communication Technology, New York State Department of Health, Wadsworth Center, Albany, NY, USA

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