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Documentation for SAMA: A method for 3D morphological analysis


Documentation for Software for Automated Morphological Analysis, a method by which epithelial structures grown in 3D cultures can be imaged, reconstructed and analyzed.


Three-dimensional (3D) culture models are critical tools for understanding tissue morphogenesis. A key requirement for their analysis is the ability to reconstruct the tissue into computational models that allow quantitative evaluation of the formed structures. Here, we present Software for Automated Morphological Analysis (SAMA), a method by which epithelial structures grown in 3D cultures can be imaged, reconstructed and analyzed with minimum human intervention. SAMA allows quantitative analysis of key features of epithelial morphogenesis such as ductal elongation, branching and lumen formation that distinguish different hormonal treatments. SAMA is a user-friendly set of customized macros operated via FIJI (http://fiji.sc/Fiji), an open-source image analysis platform in combination with a set of functions in R (http://www.r-project.org/), an open-source program for statistical analysis. SAMA enables a rapid, exhaustive and quantitative 3D analysis of the shape of a population of structures in a 3D image. SAMA is cross-platform, licensed under the GPLv3 and available at http://montevil.theobio.org/content/sama.

Keywords: Open source software, Image analysis, Ellipsoids, Morphogenesis, Computer software, Morphometry, Image processing, Branching morphogenesis

See the corresponding article.

What is SAMA?

Software for Automated Morphological Analysis or SAMA is a plugin that is operated via the imaging platform, FIJI. Although the analysis is done using R, the user-friendly interface of SAMA integrates imaging and analysis in FIJI.

If you use SAMA, please refer to the associated paper.

SAMA aims to describe morphological aspects of many objects observed in 3d, in particular but not exclusively epithelial structures in 3d culture.

SAMA is released under the Gnu Public License.

 Download SAMA (compatible with windows, mac OSX and Linux)

 Download example dataset

 Alternative, computer generated example dataset.

 Source code for the Rbind plugin

 Documentation for SAMA in pdf.


  • 22 october 2015: compatibility with version 3.5 of 3D imagej suite and better handling of errors.
  • 14 august 2015: compatibility with version 3.3 of 3D imagej suite
  • 3 may 2015: first prerelease.