ReViMS

Reconstruction and Visualization from Multiple Sections (ReViMS), an open-source, user-friendly software for automatically estimating volume and several other features of 3D multicellular aggregates (i.e., cancer spheroid, zebrafish, fruit fly).

ReViMS requires a z-stack of 2D binary masks, obtained by segmenting a sequence of fluorescent images acquired by scanning the aggregate along the z axis, using a confocal or a light-sheet fluorescent microscope. It provides a number of tools for: (a) segmenting z-stacks of fluorescence images; (b) reconstructing the 3D surface of the aggregates and estimating several features (including the volume).

ReViMS is written in MATLAB (The MathWorks, Inc., Massachusetts, USA). It is an open-source tool and the source code is freely available at: http://sourceforge.net/p/revims

Requirements: MATLAB R2017b and Image Processing Toolbox 10.1 or later versions.