<scp>SKYQUANT 3D</scp>: Quantifying Vascular Anatomy With an Open‐Source Workflow for Comprehensive Analysis of Volumetric Optoacoustic Angiography Data
Efficient visualization of the vascular system is of key importance in biomedical research into tumor angiogenesis, cerebrovascular alterations, and other angiopathies. Optoacoustic (OA) angiography offers a promising solution combining molecular optical contrast with high resolution and deep penetration of ultrasound. However, its hybrid nature implies complex data collection and processing workflows, with significant variability in methodologies across developers and users. To streamline interoperability, we introduce SKYQUANT 3D, a Python-based set of instructions for the Thermo Fisher Scientific Amira/Avizo 3D Visualization & Analysis Software. Our workflow simplifies the batch processing of volumetric optoacoustic angiography images, extracting meaningful quantitative information while also providing statistical analysis and graphical representation of the results. Quantification performance of SKYQUANT 3D is demonstrated using functional preclinical and clinical in vivo 3D OA angiographic tests involving ambient temperature variations and repositioning of the imaged limb.
Authors
- Lei Xi (ORCID: https://orcid.org/0000-0002-2598-6801)
- Anna Orlova (ORCID: https://orcid.org/0000-0002-9844-4683)
- Elizaveta Petrova
- S.V. Nemirova (ORCID: https://orcid.org/0000-0003-0142-6620)
- Marina A. Sirotkina (ORCID: https://orcid.org/0000-0002-4665-8292)
- Pavel Subochev (ORCID: https://orcid.org/0000-0001-5803-5773)
- Irina Druzhkova (ORCID: https://orcid.org/0000-0003-0293-3069)
- Alexey Kurnikov (ORCID: https://orcid.org/0000-0003-2121-2101)
- Daniel Razansky (ORCID: https://orcid.org/0000-0001-8676-0964)
- Evgeny A. Shirshin (ORCID: https://orcid.org/0000-0002-5514-3557)
- Artemii Korobov (ORCID: https://orcid.org/0009-0002-3485-1498)
- Zlata V. Besedovskaia (ORCID: https://orcid.org/0009-0008-2843-0244)
- Dmitry A. Gorin (ORCID: https://orcid.org/0000-0001-8760-615X)
- Anna Glyavina
Institutions
- Privolzhsky Research Medical University (RU)
- Skolkovo Institute of Science and Technology (RU)
- Sechenov University (RU)
- Lomonosov Moscow State University (RU)
- University of Zurich (CH)
- Southern University of Science and Technology (CN)
- ETH Zurich (CH)
- Institute for Biomedical Engineering (CH)
- Institute of Applied Physics (RU)
- N. I. Lobachevsky State University of Nizhny Novgorod (RU)
Publication Details
- Journal
- Journal of Biophotonics
- Published
- 2024-10-09
- DOI
- https://doi.org/10.1002/jbio.202400143
- Citations
- 3
- Primary Topic
- Photoacoustic and Ultrasonic Imaging
- Type
- article
- Field-Weighted Citation Impact
- 0.55
Funders
- National Natural Science Foundation of China
- Ministry of Science and Higher Education of the Russian Federation
- Swiss Cancer Research Foundation