Software tools for 3D nuclei segmentation and quantitative analysis in multicellular aggregates
| Autor: | Akos Diosdi, Nikita Moshkov, Ervin Tasnadi, Peter Horvath, Tímea Tóth, Tamas Balassa, Antonella Carbonaro, Filippo Piccinini |
|---|---|
| Přispěvatelé: | Filippo Piccinini, Tamas Balassa, Antonella Carbonaro, Akos Diosdib, Timea Toth, Nikita Moshkov, Ervin A. Tasnadi, Peter Horvath |
| Rok vydání: | 2020 |
| Předmět: |
lcsh:Biotechnology
Biophysics 3d model Review Article Machine learning computer.software_genre Biochemistry Toxicology studies 03 medical and health sciences Segmentation 0302 clinical medicine Software Phenotypic analysis Structural Biology lcsh:TP248.13-248.65 Genetics Nuclei segmentation 030304 developmental biology ComputingMethodologies_COMPUTERGRAPHICS 3D Segmentation Cancer Spheroids 0303 health sciences Microscopy business.industry 3. Good health Computer Science Applications Multicellular organism Quantitative analysis (finance) Oncology Cancer Spheroids3D 030220 oncology & carcinogenesis Single-cell Analysis Artificial intelligence business computer Biotechnology |
| Zdroj: | Computational and Structural Biotechnology Journal Computational and Structural Biotechnology Journal, Vol 18, Iss, Pp 1287-1300 (2020) |
| ISSN: | 2001-0370 |
| Popis: | Graphical abstract Today, we are fully immersed into the era of 3D biology. It has been extensively demonstrated that 3D models: (a) better mimic the physiology of human tissues; (b) can effectively replace animal models; (c) often provide more reliable results than 2D ones. Accordingly, anti-cancer drug screenings and toxicology studies based on multicellular 3D biological models, the so-called “-oids” (e.g. spheroids, tumoroids, organoids), are blooming in the literature. However, the complex nature of these systems limit the manual quantitative analyses of single cells’ behaviour in the culture. Accordingly, the demand for advanced software tools that are able to perform phenotypic analysis is fundamental. In this work, we describe the freely accessible tools that are currently available for biologists and researchers interested in analysing the effects of drugs/treatments on 3D multicellular -oids at a single-cell resolution level. In addition, using publicly available nuclear stained datasets we quantitatively compare the segmentation performance of 9 specific tools. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|