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IMAGIC ON LINUX
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DOWNLOAD

1) Download the file guiIMAGICSupervisor.AppImage

2) Create a specific IMAGIC directory (with any name you want)

3) Move the file guiIMAGICSupervisor.AppImage to this IMAGIC directory


SET THE APPIMAGE FILE PROTECTION TO EXECUTABLE

1) Open a terminal windows

2) Navigate to the IMAGIC directory (containing the file guiIMAGICSupervisor.AppImage)

3) Give the command

      chmod +x guiIMAGICSupervisor.AppImage


INSTALLATION

1) Open a terminal window

2) Navigate to the IMAGIC directory (containing the file guiIMAGICSupervisor.AppImage)

3) Give the command

      ./guiIMAGICSupervisor.AppImage --appimage-extract

   A new folder named "squashfs-root“ will be created

4) To run IMAGIC you need to define a number environment variables
   (in your .bash_profile, for example):

      export IMAGIC_ROOT=<IMAGIC directory>/squashfs-root/usr/bin/
      export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<IMAGIC directory>/squashfs-root/usr/lib/
      alias imagic=$IMAGIC_ROOT/imagic.e

      export MPIHOME=$IMAGIC_ROOT/openmpi
      export MPIBIN=$MPIHOME/bin
      export OPAL_PREFIX=$MPIHOME
      export PATH=$MPIBIN:$PATH

      where <IMAGIC directory> is the IMAGIC directory


LICENSE

1) Some of the programs are not freeware and need a license.

   If available, copy the IMAGIC license file into the IMAGIC (root) directory.

   Note: To obtain a license, please contact Image Science.


RUN IMAGIC IN TERMINAL MODE (line-by-line)

1) Open a terminal window

2) Navigate to your working directory

3) To start IMAGIC give

      imagic


RUN IMAGIC GUI PROGRAMS

- In a terminal window

     1) Navigate to your working directory

     2) Start IMAGIC:

           imagic
      
     3) Open the menu window to show all GUI programs

           IMAGIC-COMMAND : gui-supervisor

- In your browser

     Click guiIMAGICSupervisor.AppImage

- An IMAGIC menu window will open 

     Click the button of the IMAGIC GUI program you want to run
     
        Programs are: guiIMAGiC  - IMAGIC (in GUI mode)
                      guiDISPLAY - display images and sections of 3-D volumes
                      guiPLOT    - plot curves/spectra/1-D images
                      guiEM2EM   - convert 3DEM formated files
                      guiPREPARE - filter, normalise, mask, resize...
                      guiCTF     - find CTF and correct for it
                      guiMSA     - MSA and classification
                      guiFSC     - global and local resulotion
                       
                      more ...

- NOTE: When running IMAGIC in a terminal window
  
        - you can also call any GUI program by giving the related command

             IMAGIC-COMMAND : gui-...

             Examples:

                IMAGIC-COMMAND : gui-display   will open guiDISPLAY

                IMAGIC-COMMAND : gui-msa       will open guiMSA

                ...

        - you can get a list of all GUI commands by giving

             IMAGIC-COMMAND : menu *gui

        - you can get a list of all GUI commands including information by giving

             IMAGIC-COMMAND : help *gui


MANUALS

- Manuals can be found on www.ImageScience.de/manuals


CONTACT

  Image Science Software GmbH
  Kolonnenstr. 8
  D-10827 Berlin, Germany
  +49 30 8909 5326
  imagic@ImageScience.de