FARSIGHT statistics

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Citations per year

Number of citations per year for the bioinformatics software tool FARSIGHT

Tool usage distribution map

This map represents all the scientific publications referring to FARSIGHT per scientific context
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Associated diseases


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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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 citations


Robust Cell Detection for Large Scale 3D Microscopy Using GPU Accelerated Iterative Voting

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

[…] neuron is shown along the z axis.Precision-recall curves are used to compare results produced by the proposed algorithm (ivote3) to several cell localization methods and software packages, including FARSIGHT (Al-Kofahi et al., ), MINS (Lou et al., ), 3D object counter plug-in imageJ (Bolte and Cordelières, ), Laplacian of Gaussian (LoG) filter (Marr and Hildreth, ), 3D-MLS (Chinta and Wasser, ), […]


Optical clearing and fluorescence deep tissue imaging for 3D quantitative analysis of the brain tumor microenvironment

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 can be i […]


Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids

Sci Rep
PMCID: 5334646
PMID: 28255161
DOI: 10.1038/srep43693

[…] nuclei 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 segmenta […]


Employing an open source tool to assess astrocyte tridimensional structure

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

[…] tific 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, Swit […]


Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space

PLoS Comput Biol
PMCID: 4894571
PMID: 27271939
DOI: 10.1371/journal.pcbi.1004970
call_split See protocol

[…] the proposed method with five previously published methods for nucleus segmentation ( and ). Ilastik [] is based on machine learning techniques and uses image features such as Laplacian of Gaussian. FARSight [] is based on graph cut techniques. RPHC [] was designed for multi-object tracking problems such as whole-brain activity imaging of C. elegans and uses a numerical optimization-based peak de […]


Advanced light microscopy core facilities: Balancing service, science and career

Microsc Res Tech
PMCID: 5071710
PMID: 27040755
DOI: 10.1002/jemt.22648

[…] e Semantic Query User Environment, (Kvilekval et al., ) [21]) is that they are separated from the software pieces that actually do the work.Vaa3D (Visualization Assisted Analysis 3D, (Peng et al., ), FARSight ([22]) and BioImageXD (Kankaanpaa et al., ), [23]) have sophisticated volume‐rendering visualization methods and surface rendering for large 3D image data of complex biological systems like w […]

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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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