ManSegTool is an open-source software purposely developed to facilitate the manual segmentation of complex objects in a three-dimensional environment represented by image stacks. In particular, the software is constructed in a GUI framework written in Matlab that allows the user to scroll down the images constituting the stack and to manually identify the structures of interest constituting the object to segment.

The tool allows the user to:

  • iteratively zoom and draw a freehand shape representing the section of the object to be segmented
  • manually split neurites too close each other, that appear as the same structure
  • transparent overlap the original image with the i-1-th or the 1+1-th segmented one.



  • 3D stack (i.e. from confocal or two photon microscopy) in *.tiff format
  • segmented structures already processed with ManSegTool


  1. A datamatrix constituted by: i) the volumetric representation as a matrix of logical values in *.mat format, ii) the information needed to define the shape of the object surface (i.e. faces and vertices of the polygon mesh), for hard printing and iii) the time spent to perform each segmentation.
  2. A *.tiff stack in which the segmented object is highlighted within the original stack

Example of ManSegTool output