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Protocols

FluoRender specifications

Information


Unique identifier OMICS_18601
Name FluoRender
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C++, GLSL, OpenCL C
License MIT License
Computer skills Advanced
Version 2.20.1
Stability Stable
Requirements
Git, CMake, wxWidgets, Boste
Maintained Yes

Download


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Versioning


No version available

Maintainers


  • person_outline Yong Wan
  • person_outline FluoRender Team

Additional information


Manual: http://www.sci.utah.edu/releases/fluorender_v2.20/FluoRender2.20_Manual.pdf Tuto: http://www.sci.utah.edu/releases/fluorender_v2.20/FluoRender2.20_Tutorials.pdf

Publication for FluoRender

FluoRender citations

 (38)
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Layer specific morphological and molecular differences in neocortical astrocytes and their dependence on neuronal layers

2018
Nat Commun
PMCID: 5915416
PMID: 29691400
DOI: 10.1038/s41467-018-03940-3
call_split See protocol

[…] ith a laser confocal microscope (Leica TCS-SP5) equipped with an oil-immersion objective lens (×40). Confocal images were processed with Photoshop CS4 software (Adobe), the Fiji package of ImageJ, or FluoRender (University of Utah). For quantification of 3D-cell orientation, individual astrocytes were extracted with the 3D Object Counter plugin of Fiji based on the red (tdTomato) channel of confoc […]

library_books

Development of image analysis software for quantification of viable cells in microchips

2018
PLoS One
PMCID: 5832319
PMID: 29494694
DOI: 10.1371/journal.pone.0193605

[…] ds of particular cases that were subsequently extended for other purposes, such as ImageJ [], BioImageXD [], Icy [], Fiji [], Vaa3D [], CellProfiler [], 3D Slicer [], Image Slicer [], Reconstruct [], FluoRender [], ImageSurfer [], OsiriX [], and IMOD [] among others [].There are also several analytical tools already on the market. However, many of them, despite being useful for the processing of f […]

library_books

Targeted deletion of the zebrafish actin bundling protein L plastin (lcp1)

2018
PLoS One
PMCID: 5749806
PMID: 29293625
DOI: 10.1371/journal.pone.0190353

[…] ight 2-dpf embryos were collected at random, euthanized, and then bisected for microscopy and genotyping as described above. Confocal stacks were obtained on a Leica SP5 microscope and processed with FluoRender software []. […]

library_books

Internal amino acid state modulates yeast taste neurons to support protein homeostasis in Drosophila

2018
eLife
PMCID: 5812714
PMID: 29393045
DOI: 10.7554/eLife.31625.025

[…] e mounting procedure of the fly head, the labellum opens, exposing the inner surface of the labellum and the taste pegs.3D reconstructions of the nervous system and the periphery were generated using FluoRender (; ). […]

library_books

Dynamic changes in the cell membrane on three dimensional low coherent quantitative phase microscopy (3D LC QPM) after treatment with the near infrared photoimmunotherapy

2017
Oncotarget
PMCID: 5732807
PMID: 29262641
DOI: 10.18632/oncotarget.22223

[…] All LC-QPM Images were visualized using 3D-rendering software (FluoRender, University of Utah) and analyzed using Image J software. We manually traced the outline of each cell in all sliced sections and measured the cell volume using Image J which was compared to […]

library_books

Odd skipped related 1 identifies a population of embryonic fibro adipogenic progenitors regulating myogenesis during limb development

2017
Nat Commun
PMCID: 5662571
PMID: 29084951
DOI: 10.1038/s41467-017-01120-3

[…] bs was performed as previously described. For 3D reconstruction, images captured on a LSM710 confocal microscope (Zeiss) were analysed using the programs Amira® (FEI visualization Sciences Group) and Fluorender® (University of Utah). […]

Citations

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FluoRender institution(s)
Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Department of Bioengineering, University of Utah, Salt Lake City, UT, USA; Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan; Department of Biology, University of Florida, Gainesville, FL, USA; Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
FluoRender funding source(s)
Supported by the R01-GM098151-01, NIH P41 GM103545-18, NSF ACI-1339881, and NSF IIS-1162013.

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