QUINT-ONLINE WORKFLOW: PERSONALISED WORKING ENVIRONMENT FOR ATLAS-BASED ANALYSES OF BRAIN SECTION IMAGES IN RODENTS

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/.
“Funded from the European Union’s Research and Innovation Program Horizon Grant Agreement No. 101147319 (EBRAINS 2.0).”