Arda Balkir

• Puchades, Maja; Yates, Sharon Christine; Csucs, Gergely; Carey, Harry Alexander Chandler; Balkir, Arda & Leergaard, Trygve B. [Show all 7 contributors for this article] (2025). Software and pipelines for registration and analyses of rodent brain image data in reference atlas space. Frontiers in Neuroinformatics. 19, p. 1–15. doi: 10.3389/fninf.2025.1629388. Full text in Research Archive Show summary

  Advancements in methodologies for efficient large-scale acquisition of high-resolution serial microscopy image data have opened new possibilities for experimental studies of cellular and subcellular features across whole brains in animal models. There is a high demand for open-source software and workflows for automated or semi-automated analysis of such data, facilitating anatomical, functional, and molecular mapping in healthy and diseased brains. These studies share a common need to consistently identify, visualize, and quantify the location of observations within anatomically defined regions, ensuring reproducible interpretation of anatomical locations, and thereby allowing meaningful comparisons of results across multiple independent studies. Addressing this need, we have developed a suite of desktop and web-applications for registration of serial brain section images to three-dimensional brain reference atlases (QuickNII, VisuAlign, WebAlign, WebWarp, and DeepSlice) and for performing data analysis in a spatial context provided by an atlas (Nutil, QCAlign, SeriesZoom, LocaliZoom, and MeshView). The software can be utilized in various combinations, creating customized analytical pipelines suited to specific research needs. The web-applications are integrated in the EBRAINS research infrastructure and coupled to the EBRAINS data platform, establishing the foundation for an online analytical workbench. We here present our software ecosystem, exemplify its use by the research community, and discuss possible directions for future developments.

• Puchades, Maja; Yates, Sharon Christine; Csucs, Gergely; Carey, Harry; Balkir, Arda & Leergaard, Trygve B. [Show all 7 contributors for this article] (2025). Software and pipelines for registration and analyses of rodent brain image data in reference atlas space. bioRxiv. ISSN 2692-8205. Full text in Research Archive

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• Balkir, Arda; Yates, Sharon Christine; Csucs, Gergely; Leergaard, Trygve B.; Puchades, Maja & Bjaalie, Jan G. (2026). QUINT-ONLINE WORKFLOW: PERSONALISED WORKING ENVIRONMENT FOR ATLAS-BASED ANALYSES OF BRAIN SECTION IMAGES IN RODENTS. doi: https:/fens2026.abstractserver.com/program/#%2Fdetails%2Fpresentations%2F4213. Full text in Research Archive Show summary

  Studies of the cellular architecture and neural connections in the brain often rely on histology-based methods in rodent wild type and disease models. Registration of brain section images to a reference brain atlas has become the standard for obtaining high quality and precise data, allowing comparison and integration of disparate data within a standardised coordinate system. While a few analytical tools are available to researchers, barriers to uptake, such as coding skill requirements, data type limitations, and insufficient documentation are still present. We have developed an intuitive, reliable and versatile solution for enabling such analyses. The QUINT-online workflow combines the use of a series of web-applications (CreateZoom, WebAlign, WebWarp, Webilastik, WebNutil and MeshView) integrated in an online platform, accessible with an EBRAINS account. It builds on the QUINT workflow (Yates et al. 2019, doi: 10.3389/fninf.2019.00075) using desktop applications, which has been used widely by the research community for cell counting, tract tracing studies and for analysis of tissue clearing data. This new online solution allows researchers to register heterogeneous image series to reference brain atlases, to identify features to quantify, and to perform brain-wide mapping and quantification, on a user-friendly platform. The QUINT-online workflow benefits from simplified file management steps and new features such as microscopy viewer links and automated mapping of selected objects. EBRAINS users can already access a beta version at https://quint-online.apps.ebrains.eu/.

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