2022-03-10T12:07:06 n57599

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

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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.


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 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.

Publications

Jaeschke A, Eckert H, Bray LJ. Qiber3D-an open-source software package for the quantitative analysis of networks from 3D image stacks. Gigascience. 2022 Feb;11. DOI: 10.1093/gigascience/giab091. PMID: 35134926; PMCID: PMC8848317. https://europepmc.org/article/MED/35134926

Research areas

Biomedical engineering
Image processing
Other physical sciences

Cite this collection

Jaeschke, Anna; Eckert, Hagen; Bray, Laura J; (2021): Qiber3D - an open-source software package for the quantitative analysis of networks from 3D image stacks. Queensland University of Technology. (Software) https://doi.org/10.25912/RDF_1646370223982

Related information

Partner institution

Duke University, Durham, NC. USA https://duke.edu/

Licence

MIT License

Copyright

© Queensland University of Technology, Anna Jaeschke and Hagen Eckert, 2021.

Data file types

*.tiff, *.tif, *.nd2, and other proprietary file formats to store microscopy data

Dates of development

From 2021-01-28 to 2021-10-25

Connections

Has association with
Laura Bray  (Researcher)

Contacts

Other

Date record created:
2021-12-10T11:27:17
Date record modified:
2022-03-10T12:07:06
Record status:
Published - Open Access