SAMA documentation - Installation of SAMA
Documentation for Software for Automated Morphological Analysis : Installation of SAMA and its dependencies.
See the article.
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.
- 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.
- 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.
SAMA documentation - How to use SAMA?