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SAMA documentation - Installation of SAMA

Documentation for Software for Automated Morphological Analysis : Installation of SAMA and its dependencies.


Dependencies

Programs required:

If they are not already installed, install FIJI and R.

WARNING for Microsoft Windows users: it is better to install R and fiji outside Program Files to avoid problems of permissions.

FIJI Plugins required:

Optional FIJI Plugins:

Installation of Sama

  • Download SAMA:  http://montevil.theobio.org/sites/montevil.theobio.org/files/sama/Sama.zip
  • Extract Sama.zip and copy the SAMA folder in the plugins folder of FIJI.
  • (Re)start FIJI.
  • In FIJI , run Plugin>Sama>install or update R component. Then select install in the dialog and hit ok. This process will install the required R packages, including the R SAMA components.
  • Windows only: SAMA will ask you for the path to the R executable. It usually is in /root folder/R/R-x.x.x/bin/. In case of a mistake, it is possible to change this path in SAMA > updateR. Let us recall that R should not be installed in Program files because of issues with permissions.

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