Longitudinal three-photon imaging for tracking amyloid plaques and vascular degeneration in a mouse model of Alzheimer’s disease

Vascular abnormalities may contribute to amyloid-beta accumulation and neurotoxicity in Alzheimer’s disease (AD). Monitoring vascular degeneration as AD progresses is essential. Three-photon fluorescence microscopy (3PM) enables high-resolution deep tissue imaging with minimal invasiveness and photodamage. We demonstrated the potential of three-photon imaging to track vascular and amyloid-related changes in deep cortical structures. It offers a tool for studying the interplay between vascular and amyloid pathologies in AD, supporting future research into disease mechanisms and therapeutic strategies. This dataset contains all three-photon imaging data used in the manuscript, including plaques and vascular structures across multiple mice, fields of view (FOVs), and two longitudinal imaging sessions. GFP labeled neurons with vessels as well as neonatal lung imaging for power calibration can also be found in the folder.
, , # Data from: Longitudinal three-photon imaging for tracking amyloid plaques and vascular degeneration in a mouse model of Alzheimer’s disease

Dataset DOI: 10.5061/dryad.wh70rxx2j

## Description of the data and file structure

The data were collected for a study using longitudinal three-photon microscopy to monitor changes in blood vessels and amyloid plaques in APP NL-G-F mice. Mice were imaged twice, four weeks apart. Texas Red labeled the vasculature, and methoxy-XO4 labeled amyloid plaques. Three-photon imaging enabled deep cortical imaging, and the resulting stacks were processed to segment vessels and plaques and to quantify structural changes over time.

This dataset (wetransfer_data-3p_2025-11-21_1143.zip) also includes one stack of GFP-labeled neurons with vessels, two additional plaque–vessel stacks, and six neonatal lung images used for power calibration.

### Files and variables

All files are TIFF image stacks (16-bit grayscale).

**1. Fig 3**

XY pixel size 0.98 µm; Z-ste...,