imagej
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imagej [2011/09/13 17:12] 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 (including the three mentioned below) 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. | ||
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| + | 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 === | ||
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| * Susanne Rafelski has put together a nice guide to getting started with ImageJ: [[ImageJ Introduction|ImageJ Introduction]] | * 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]] | * Micro-manager has a [[http://valelab.ucsf.edu/~MM/MMwiki/index.php/Micro-Manager_User%27s_Guide|User's Guide]] | ||
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| + | === 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 | ||
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