NeuroFlow
A complete, browser-based pipeline for mapping labeled cells in histological brain sections onto a reference atlas — from raw images to region-by-region cell counts, all in one window.
What it does
NeuroFlow guides you through the full workflow of quantifying fluorescently labeled cells across the mouse brain. Import your section images, align them to the Allen Brain Atlas, detect labeled cells, and get a clean, exportable table of cell counts for every brain region — no coding required.
How it works — five simple steps
Cropper
Import your section images (PNG / JPG / WebP / BMP) and crop them to the tissue.
Arranger
Order your sections along the rostral–caudal axis of the brain.
Scaler
Register each section to its matching coronal atlas plate to assign brain regions.
Quantifier
Detect labeled cells and place them onto the registered atlas coordinates.
Analyzer
Review per-region cell counts on a 3D brain and export the results to Excel.
Highlights
Quick start
Click Launch NeuroFlow, then drag your first section image into the Cropper. Follow the tabs left to right — Cropper → Arranger → Scaler → Quantifier → Analyzer — and export your region counts at the end. The tool remembers your work between steps.