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bioRxiv · 10.64898/2026.07.15.737186

NeuroFlow: An Integrated, Cross-Platform Workflow for Mouse Brain Atlas Registration and Quantification

Rao, A.·Oo, H. Z.·Tao, C.·Zhang, G.-W.
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Abstract

Registration of histological sections to a reference atlas is essential for anatomical localization and region-based quantitative analysis. Although established workflows are powerful, image preparation, registration, quantification, and visualization often rely on multiple software packages, some of which require platform-specific installation or locally configured programming environments. Here, we present NeuroFlow, a browser-based workflow for quantitative analysis of mouse brain histology. NeuroFlow integrates image registration, signal detection, quantification, and visualization within a single interface and operates across major operating systems without additional software installation. It supports affine and nonlinear alignment, as well as real-time oblique reslicing of the reference atlas. All processing is performed locally in a desktop browser, without requiring a local Python environment, MATLAB installation, or associated packages and toolboxes, and without uploading images to a remote server. This design preserves user control over data and keeps intermediate results accessible for inspection and review. NeuroFlow is available at https://guangweizhang.com/tool-neuroflow.html.

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Rao, A., Oo, H. Z., Tao, C., Zhang, G.-W.. 2026-07-20. NeuroFlow: An Integrated, Cross-Platform Workflow for Mouse Brain Atlas Registration and Quantification. https://doi.org/10.64898/2026.07.15.737186

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