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Vision Science Research Center School of Optometry | School of Medicine

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VSRC Links



https://micro-manager.org/ μmanager home page, software to control automated microscopes

https://open-imaging.com/ not-for-profit company that now runs μmanager (sign up here for news updates)

https://micro-manager.org/wiki/Micro-Manager_User%27s_Guide μmanager user’s guide

https://micro-manager.org/wiki/Plugins μmanager plugins

http://www.jbmethods.org/jbm/article/view/36/29 linc to manuscript describing advanced methods of microscope control using μmanager

https://micro-manager.org/wiki/Micro-Manager_Programming%20Guide programming μmanager in general and to work with other software such as Matlab

https://micro-manager.org/wiki/Micro-Manager_Community μmanager user community for open discussion of the use of the software


http://icy.bioimageanalysis.org/ open source stand-alone image analysis

http://icy.bioimageanalysis.org/plugin/list icy plugin list

http://icy.bioimageanalysis.org/script/list icy script list

http://icy.bioimageanalysis.org/protocol/list icy protocol list

http://icy.bioimageanalysis.org/download icy download


http://mosaic.mpi-cbg.de/?q=downloads/imageJ a suite of imagej plugins for image processing (available in our fiji2-μmanager build)


http://bigwww.epfl.ch/deconvolution/deconvolutionlab2/ 2D/3D deconvolution of fluorescence images with numerous choice of algorithm

http://bigwww.epfl.ch/algorithms/psfgenerator/ creates point spread functions for deconvolution (available in our fiji2-μmanager build)

 -CoolLED pe-4000 light source 









https://www.zeiss.com/corporate/int/home.html Our microscope is the Axioplan 2

-Excelitas X-Cite 120LEDBoost

http://www.excelitas.com/Pages/Product/X-Cite-120LEDBoost.aspx our fluorescence LED light source


Zeiss Axioplan 2 imaging microscope manual

Zeiss Axiovision Software manual

Zeiss Apotome software manual

DeconvoltuionLab2 Published description in the journal Methods 

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