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imagej [2011/01/31 12:32]
kthorn
imagej [2015/04/16 16:57]
kthorn
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 [[http://​rsbweb.nih.gov/​ij/​|ImageJ]] is one of the older free, open source image analysis programs. ​ Alone, it's not that powerful; it's real strength is the vast array of plugins for it.  It runs on Windows, Mac, and Linux. [[http://​rsbweb.nih.gov/​ij/​|ImageJ]] is one of the older free, open source image analysis programs. ​ Alone, it's not that powerful; it's real strength is the vast array of plugins for it.  It runs on Windows, Mac, and Linux.
  
-[[http://pacific.mpi-cbg.de/​wiki/​index.php/​Fiji|FIJI]] is probably the best disctribution ​of ImageJ for routine data analysis. ​ It comes with a vast array of plugins already installed and ready to use and has an automatic updater so you always have the latest versions of them.+[[http://fiji.sc|FIJI]] is probably the best distribution ​of ImageJ for routine data analysis. ​ It comes with a vast array of plugins already installed and ready to use (including the three mentioned below) ​and has an automatic updater so you always have the latest versions of them.
  
 [[http://​www.micro-manager.org/​|Micro-Manager]] is a microscope control package that is built on top of ImageJ. ​ It's developed at UCSF and is very powerful; we use it to control the Spinning Disk Confocal in the Nikon Imaging Center. [[http://​www.micro-manager.org/​|Micro-Manager]] is a microscope control package that is built on top of ImageJ. ​ It's developed at UCSF and is very powerful; we use it to control the Spinning Disk Confocal in the Nikon Imaging Center.
 +
 +A tutorial on getting started with micro-manager:​ http://​www.youtube.com/​watch?​v=y-R9WmhzPdI&​feature=related
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 +
 +A screen cast tutorial on multi dimensional acquisition using micro-manager:​ http://​www.youtube.com/​watch?​v=6LoKX6Eect0
  
 === Plugins === === Plugins ===
 The following plugins may be of particular interest to NIC users: The following plugins may be of particular interest to NIC users:
 +
 [[http://​valelab.ucsf.edu/​~nico/​IJplugins/​Ics_Opener.html|ICS Opener]] - Allows ImageJ to open ICS files from the Nikon C1 confocal. [[http://​valelab.ucsf.edu/​~nico/​IJplugins/​Ics_Opener.html|ICS Opener]] - Allows ImageJ to open ICS files from the Nikon C1 confocal.
  
 +[[http://​rsbweb.nih.gov/​ij/​plugins/​nd2-reader.html|ND2 Reader]] - Opens NIS-Elements ND2 files (old, may be outdated).
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 +[[http://​www.loci.wisc.edu/​software/​bio-formats|Bioformats]] - Library for reading many microscopy file types, including ICS and ND2.  Probably preferred to the ND2 reader above.
 +
 +=== Documentation ===
 +  * Susanne Rafelski has put together a nice guide to getting started with ImageJ: [[ImageJ Introduction|ImageJ Introduction]]
 +  * Micro-manager has a [[http://​valelab.ucsf.edu/​~MM/​MMwiki/​index.php/​Micro-Manager_User%27s_Guide|User'​s Guide]]
 +
 +=== Learning ===
 +{{:​image_analysis_lab_manual.pdf|Here is a self-guided tutorial on image processing in ImageJ/​Fiji}}. ​
  
 === Miscellaneous === === Miscellaneous ===
 If you do a lot of work with ImageJ, you may want to subscribe to the ImageJ mailing list: http://​rsbweb.nih.gov/​ij/​list.html If you do a lot of work with ImageJ, you may want to subscribe to the ImageJ mailing list: http://​rsbweb.nih.gov/​ij/​list.html
/var/www/html/dokuwiki/data/pages/imagej.txt · Last modified: 2015/04/16 16:57 by kthorn