SAMA documentation - Installation of SAMA

Dependencies

Programs required:

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

• FIJI - http://fiji.sc/Installation
• R - http://cran.r-project.org/

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

FIJI Plugins required:

• 3D imageJ suite http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start.
  As of now, Sama is compatible with version 3.5 and later.
  This plugin can be installed by going to help> update fiji. And in the new window going to Manage update sites and activating the 3D ImageJ Suite.

Optional FIJI Plugins:

• BoneJ http://bonej.org/#install
• Puredenoise http://bigwww.epfl.ch/algorithms/denoise/

Installation of Sama

• Download SAMA:  http://montevil.org/assets/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.