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Open AccessFeature PaperArticle

Open-Source Tools for Volume Estimation of 3D Multicellular Aggregates

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Advanced Research Center on Electronic Systems (ARCES) for Information and Communication Technologies “E. De Castro”, University of Bologna, I-40125 Bologna, Italy
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Interdepartmental Centre “L. Galvani” for Integrated Studies of Bioinformatics, Biophysics & Biocomplexity (CIG), University of Bologna, I-40125 Bologna, Italy
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Synthetic and System Biology Unit, Hungarian Academy of Sciences, Biological Research Centre (BRC), H-6726 Szeged, Hungary
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Institute for Molecular Medicine Finland, University of Helsinki, FI-00014 Helsinki, Finland
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Department of Computer Science and Engineering (DISI), University of Bologna, I-40126 Bologna, Italy
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Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, I-47014 Meldola (FC), Italy
*
Author to whom correspondence should be addressed.
Appl. Sci. 2019, 9(8), 1616; https://doi.org/10.3390/app9081616
Received: 12 March 2019 / Revised: 3 April 2019 / Accepted: 10 April 2019 / Published: 18 April 2019
(This article belongs to the Section Applied Biosciences and Bioengineering)
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. View Full-Text
Keywords: oncology; microscopy; 3D in vitro models; surface rendering; volume estimation oncology; microscopy; 3D in vitro models; surface rendering; volume estimation
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De Santis, I.; Tasnadi, E.; Horvath, P.; Bevilacqua, A.; Piccinini, F. Open-Source Tools for Volume Estimation of 3D Multicellular Aggregates. Appl. Sci. 2019, 9, 1616.

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