Qiber3D—an open-source software package for the quantitative analysis of networks from 3D image stacks

BACKGROUND: Optical slice microscopy is commonly used to observe cellular morphology in 3D tissue culture, e.g., the formation of cell-derived networks. The morphometric quantification of these networks is essential to study the cellular phenotype. Commonly, the quantitative measurements are performed on 2D projections of the image stack, resulting in the loss of information in the third dimension. Currently available 3D image analysis tools rely on manual interactions with the software and are therefore not feasible for large datasets. FINDINGS: Here we present Qiber3D, an open-source image processing toolkit. The software package includes the essential image analysis procedures required for image processing, from the raw image to the quantified data. Optional pre-processing steps can be switched on/off depending on the input data to allow for analyzing networks from a variety of sources. Two reconstruction algorithms are offered to meet the requirements for a wide range of network types. Furthermore, Qiber3D’s rendering capabilities enable the user to inspect each step of the image analysis process interactively to ensure the creation of an optimal workflow for each application. CONCLUSIONS: Qiber3D is implemented as a Python package, and its source code is freely available at https://github.com/theia-dev/Qiber3D. The toolkit was designed using a building block principle to enable the analysis of a variety of structures, such as vascular networks, neuronal structures, or scaffolds from numerous input formats. While Qiber3D can be used interactively in the Python console, it is aimed at unsupervised automation to process large image datasets efficiently.