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EMBL BioImage Data Analysis



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RT @COST_INDEPTH: Superb online training event provided by the @NEUBIAS_COST Academy, beginning on April 14th with a course on ImageJ/Fiji…
About 27 mins, 12 secs ago by: Kota Miura (@cmci_)

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RT @NEUBIAS_COST: Attention to the Bioimaging community: The NEUBIAS Academy starts with online training events h…
About 19 hours, 55 mins ago by: Kota Miura (@cmci_)

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RT @PavelTomancak: Whoa!
About 3 days, 2 hours ago by: Kota Miura (@cmci_)

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About 5 days ago by: Kota Miura (@cmci_)

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@e_petsalaki @GallegoLab @marko_kaksonen @Biosdfp @taraskalab @AndrewPlested @giraldezT @PeyingFong @ScottKFerguson
About 1 week, 3 days ago by: Kota Miura (@cmci_)

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.. I think that was a wrong link, here we go: COvid19 RESPirator OpeN SourcE #COVID19
About 1 week, 3 days ago by: Kota Miura (@cmci_)

OSX software (2013.07.17)

Here is a list of installed software in OSX mountain lion machine.
I leave this as a memo, mostly for myself.

  • google chrome
  • chrome app
    • simplenote
    • evernote
    • dropbox
    • google japanese input
    • google calender
    • google tasks
    • diigo
    • white spaces
  • Google Notifier
    • For setting gmail as default mail client.
  • DropBox, desktop
  • Evernote, desktop
  • istat pro (dashboard gadget)
    • This allows quick view (command-space) to automatically show ZIP contents
  • Xcode
    • install Git
    • add /user/local path to the .bash_profile
    • install python (2.7.3)
      • followed instruction here
      • then with python pip, install numpy, scipy, matplotlib
      • IPython (instruction)
        • brew install pyqt
    • macvim
      • brew install macvim –override-system-vim
    • maven
      • ln -sf ../Cellar/jython/2.5.3/libexec/jython /usr/local/bin/jython
        • this is required for interactive shell.
      • M2_PATH=~/.m2/repository
        JYTHONPATH=`find $M2_PATH -name “*.jar” | tr “\\n” “:“`
        export JYTHONPATH
      • sbt
    • brew linkapps
    • R
      • brew install R
        • sudo mv /Library/Frameworks/R.framework /Library/Frameworks/native_R.framework
        • sudo ln -s ”/usr/local/Cellar/r/2.15.1/R.framework” /Library/Frameworks
        • defaults write org.R-project.R force.LANG en_US.UTF-8
    • ffmpeg
    • wget
    • openCV
      • brew install opencv
    • bash-completion
    • ctags
      • ln -s ~/<>/config/dotfiles/ctags ~/.ctags
    • newsbeuter
  • Eclipse
  • RStudio (linked to homebrew R)
  • Fiji & ImageJ
  • Tex related (instructions)
    • brew install ghostscript
    • brew install imagemagick
    • MacTeX.pkg > double click, in “customoize” select only text live 2012 and GUI package
    • ln -s /usr/local/Cellar/r/3.0.1/R.framework/Versions/3.0/Resources/share/texmf/tex/latex ~/Library/texmf/tex/
      • this is to link sweave style file to tex.
  • Mendeley Desktop
    • sync reference pdf and database via dropbox
        • ~/Library/Application Support>cp -r Mendeley\ Desktop ~/Dropbox/Mendeley/db/
        • ~/Library/Application Support>mv Mendeley\ Desktop _backup_Mendeley\ Desktop
        • ln -s ~/Dropbox/Mendeley/db/Mendeley\ Desktop
    • PDF viewer, that could be in sync with texlipse (tex editor)
    • Universal video viewer.
    • addons
      • TuneIn, an internet radio tuner.
    • swiss army knife for document conversion.
    • osx application uninstaller
    • SFTP. I sometime use this for transfering many files across servers
  • Copy File Path
    • customize a Finder service,, that adds a shortcut key (command-shift-c) to copy full path into clipboard.
  • LibreOffice
  • Skype
  • Fonts
  • IgorPro (Wavemetrics, not free)
  • Parallel (not free)
    • Windows7 (not free)
    • Chrome OS
  • MS office standard (not free) + endnote (not free)
  • Adobe CS package (not free)
  • pending: some adjustments needed needed
documents/120905osxinstallation.txt · Last modified: 2016/05/24 05:46 (external edit)