Data from: Longitudinal three-photon imaging for tracking amyloid plaques and vascular degeneration in a mouse model of Alzheimer’s disease
Data files
Dec 12, 2025 version files 2.67 GB
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README.md
2.42 KB
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wetransfer_data-3p_2025-11-21_1143.zip
2.67 GB
Abstract
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.
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-step 5 µm (plaques/vessels), 10 µm (neurons); channels: Texas Red, methoxy-XO4, GFP, THG.
- 3a Plaques.tif – Methoxy-XO4 plaques
- 3a Vessels.tif – Texas Red vessels
- 3b GFP neurons.tif – GFP-labeled neurons with vessels
2. Longitudinal Imaging
Each mouse was imaged twice, 4 weeks apart (Session 1 and Session 2).
XY pixel size 0.98 µm; Z-step 5 µm; depth ~0–900 µm; excitation 1340 nm. Texas Red (vessels), methoxy-XO4 (plaques)
Mouse 1 FOV I
- Plaques S1, Plaques S2
- Vessels S1, Vessels S2
Mouse 1 FOV II
- Plaques S1, Plaques S2
- Vessels S1, Vessels S2
Mouse 2 FOV I
- Plaques S1, Plaques S2
- Vessels S1, Vessels S2
Mouse 2 FOV II
- Plaques S1, Plaques S2
- Vessels S1, Vessels S2
Mouse 3 FOV I
- Plaques S1 (if present), Plaques S2
- Vessels S1, Vessels S2
3. Calibration Data
XY pixel size 0.98 µm; Z-step 5 µm; used for power-stability checks.
- neonatal_lung_sampleA1–A3.tif
- neonatal_lung_sampleB1–B3.tif
4. High-plaque load test images
XY pixel size 0.98 µm; Z-step 5 µm; depth ~0–900 µm; excitation 1340 nm. Texas Red (vessels), methoxy-XO4 (plaques)
- Vessels plus plaques.tif
- Vessels plus plaques 2.tif
Code/software
All data can be viewed and processed using the codes accessible on:
https://github.com/estassss/Longitudinal-three-photon-imaging