Open-source tools for volume estimation of 3D multicellular aggregates

Ilaria De Santis, Ervin Tasnadi, Peter Horvath, Alessandro Bevilacqua, Filippo Piccinini

Research output: Contribution to journalArticlepeer-review


The volume is one of the most relevant features that define the treatment of an in vivo tumour. When using cancer 3D in vitro models in pre-clinical studies, it becomes important to evaluate the macroscopic effects of drugs and radiotherapy treatments. Depending on the nature of the 3D in vitro model used, different open-source solutions can be used for measuring the volume by starting from microscope-acquired images. In this work, we introduced several open-source tools today available for estimating the volume of 3D multicellular aggregates (e.g., spheroids, organoids), also giving hints for defining the "best software" by analysing characteristics of 3D in vitro models and limits of the tools. Finally, using several cancer organoids imaged by a fluorescent microscope, we compared volume estimations obtained with different tools, besides presenting a new version of the Reconstruction and Visualization from Multiple Sections (ReViMS version 2.0) tool. This work aims to be the reference for researchers interested in estimating the volume of 3D multicellular aggregates through an open-source tool.

Original languageEnglish
Article number1616
JournalApplied Sciences (Switzerland)
Issue number8
Publication statusPublished - Apr 2019


  • 3D in vitro models
  • Microscopy
  • Oncology
  • Surface rendering
  • Volume estimation

ASJC Scopus subject areas

  • Materials Science(all)
  • Instrumentation
  • Engineering(all)
  • Process Chemistry and Technology
  • Computer Science Applications
  • Fluid Flow and Transfer Processes


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