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Updated: Dec 16, 2025

Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Published on: November 7, 2025

Software tools for 3D nuclei segmentation and quantitative analysis in multicellular aggregates.

Filippo Piccinini¹, Tamas Balassa², Antonella Carbonaro³

¹Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Cancer Research Hospital, Meldola, FC, Italy.

Computational and Structural Biotechnology Journal

|July 3, 2020

Summary

This summary is machine-generated.

3D biology models like organoids offer better human tissue mimicry for drug screening. This study reviews free software tools for analyzing single-cell behavior in these complex 3D models.

Keywords:

3D Segmentation Cancer Spheroids Microscopy Oncology Single-cell Analysis

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Last Updated: Dec 16, 2025

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Staining and High-Resolution Imaging of Three-Dimensional Organoid and Spheroid Models

Staining and High-Resolution Imaging of Three-Dimensional Organoid and Spheroid Models

Published on: March 27, 2021

Area of Science:

* 3D Biology and Tissue Engineering
* Pharmacology and Toxicology
* Bioinformatics and Computational Biology

Background:

* Three-dimensional (3D) biological models, including spheroids, tumoroids, and organoids, are increasingly used in research due to their superior mimicry of human physiology compared to traditional 2D models.
* These advanced models offer potential replacements for animal testing and yield more reliable results in drug screening and toxicology studies.
* Analyzing individual cell behavior within complex 3D structures presents significant challenges due to limitations in manual quantitative analysis.

Purpose of the Study:

* To identify and describe freely accessible software tools for analyzing the effects of drugs and treatments on 3D multicellular models at a single-cell resolution.
* To quantitatively compare the performance of nine specific segmentation tools using publicly available nuclear-stained datasets.

Main Methods:

* Literature review and compilation of currently available free software tools for 3D multicellular model analysis.
* Quantitative comparison of segmentation performance of selected tools on nuclear-stained 3D biological datasets.

Main Results:

* A comprehensive overview of accessible software tools for single-cell analysis in 3D biological models is provided.
* The study presents a comparative analysis of the segmentation accuracy of nine different software tools.

Conclusions:

* The development and accessibility of advanced software tools are crucial for overcoming the analytical challenges posed by complex 3D biological models.
* This work aids researchers in selecting appropriate tools for phenotypic analysis in 3D drug screening and toxicology studies, facilitating more robust and reliable experimental outcomes.