Data from: Impact of aging on neck vasculature and brain biochemistry in female mice
Data files
Sep 22, 2026 version files 7.88 GB
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C57_Female_US_measurements.xlsx
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cc_c57_brain_yfm_ofm_young_neg_60.imzML
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cc_c57_brains_yfm_ofm_old_neg_60micron.imzML
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cc_c57_brains_yfm_ofm_old_pos_60micron.imzML
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cc_c57_brains_yfm_ofm_pos_60micron.imzML
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cc_c57_brains_yfm_ofm_young_pos_60micron.imzML
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cc_c57_rjug_dfm_yfm_pos_10micron.imzML
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cc_jug_c57_yfm_ofm_neg_10micron.imzML
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cc_r_car_c57_yfm_dfm_3_5_10micron_neg.imzML
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cc_r_car_c57_yfm_ofm_4_8_10micron_neg.imzML
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OFM_C57_RJUG_section_1.nd2
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OFM_C57_RJUG_section_2.nd2
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OFM_C57_RJUG_section_3.nd2
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OFM_C57_RJUG_section_4_(1).nd2
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OFM_C57_RJUG_section_5.nd2
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OFM_CAR_1_3a_20x_bottom.tif
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OFM_CAR_1_3a_20x_top.tif
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OFM_CAR_1_3a_20x.tif
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OFM_CAR_1_3a.tif
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OFM_CAR_1_3b.tif
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OFM_CAR_1_3c_20x.tif
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OFM_CAR_1_3c.tif
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OFM_CAR_4-5_a.tif
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OFM_CAR_4-5_b.tif
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OFM_CAR1_3a_ch00.tif
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OFM_CAR1_3a_ch01.tif
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OFM_CAR1_3a_overlay.tif
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OFM_CAR1_3b_ch00.tif
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OFM_CAR1_3b_ch01.tif
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OFM_CAR1_3b_overlay.tif
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OFM_CAR1_3c_ch00.tif
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OFM_CAR1_3c_ch01.tif
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OFM_CAR1_3c_overlay.tif
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OFM_CAR4_5a_ch00.tif
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OFM_CAR4_5a_ch01.tif
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OFM_CAR4_5a_overlay.tif
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OFM_CAR4_5b_ch00.tif
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OFM_CAR4_5b_ch01.tif
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OFM_CAR4_5b_overlay.tif
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OFM_Jug_a_bottom.tif
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OFM_Jug_a_top.tif
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OFM_Jug_b_bottom_2.tif
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OFM_Jug_b_bottom.tif
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OFM_Jug_b_top_2.tif
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OFM_Jug_b_top.tif
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OFM_Jug_c_below.tif
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OFM_Jug_c.tif
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OFM_Jug_d_bottomright.tif
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OFM_Jug_d_topright.tif
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OFM_Jug_d.tif
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OFM_Jug_e_left.tif
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OFM_Jug_e.tif
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README.md
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YFM_C57_RJUG_4_section_1.nd2
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YFM_C57_RJUG_4_section_2.nd2
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YFM_C57_RJUG_4_section_3.nd2
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YFM_C57_RJUG_4_section_4.nd2
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YFM_C57_RJUG_4_section_5.nd2
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YFM_CAR_1_3a.tif
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YFM_CAR_1_3b_bottom.tif
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YFM_CAR_1_3b_top.tif
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YFM_CAR_1_3b.tif
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YFM_CAR_1_3c.tif
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YFM_CAR_4_5a.tif
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YFM_CAR_4_5b.tif
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YFM_CAR1_3_20x_ch00.tif
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YFM_CAR1_3_20x_ch01.tif
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YFM_CAR1_3_20x_overlay.tif
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YFM_CAR1_3_ch00.tif
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YFM_CAR1_3_ch01.tif
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YFM_CAR1_3_overlay.tif
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YFM_CAR1_3b_ch00.tif
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YFM_CAR1_3b_ch01.tif
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YFM_CAR1_3b_overlay.tif
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YFM_CAR1_3c_ch00.tif
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YFM_CAR1_3c_ch01.tif
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YFM_CAR1_3c_overlay.tif
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YFM_CAR1_45a_ch00.tif
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YFM_CAR1_45a_ch01.tif
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YFM_CAR1_45a_overlay.tif
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YFM_CAR1_45b_ch00.tif
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YFM_CAR1_45b_ch01.tif
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YFM_CAR1_45b_overlay.tif
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YFM_Jug_a_top.tif
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YFM_Jug_a.tif
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YFM_Jug_b_bottom.tif
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YFM_Jug_b_lower.tif
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YFM_Jug_b_top.tif
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YFM_Jug_c.tif
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YFM_Jug_d.tif
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YFM_Jug_e_top.tif
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YFM_Jug_e.tif
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Abstract
This dataset contains raw and processed data supporting a study of age-related neurovascular and biochemical changes in female mice. Files include in vivo ultrasound measurements of carotid artery and jugular vein structure and hemodynamics, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) data from brain and vascular tissues, and histology images from vascular sections. Ultrasound data include vessel diameter, systolic and diastolic velocity, wall shear stress, circumferential cyclic strain, pulsatility index, and volumetric flow measurements. MALDI-MSI files include ion images, peak lists, and associated spectral outputs used to evaluate lipid distributions in brain, carotid artery, and jugular vein tissue. Histology files include representative and quantified images from stains used to assess vascular wall composition, including elastin- and collagen-associated features. Together, these data support analyses of age-dependent changes in vascular biomechanics, extracellular matrix remodeling, and lipid biochemistry across tissues. The dataset is organized to enable reproduction of the reported figures, statistical analyses, and exploratory comparisons between young and middle-aged groups.
This dataset contains multimodal imaging, lipidomics, and ultrasound data collected to investigate age-related changes in the neurovascular system of female C57BL/6 mice. Young (12-week-old) and aged (52-week-old) mice underwent in vivo ultrasound imaging followed by tissue collection for matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), liquid chromatography-mass spectrometry (LC-MS) lipidomics, and fluorescence microscopy of the brain, carotid artery, and jugular vein.
Abbreviations
| Abbreviation | Definition |
|---|---|
| YFM | Young Female Mouse (12 weeks) |
| OFM | Old Female Mouse (52 weeks) |
| C57 | C57BL/6NHsd mouse strain |
| CAR | Carotid artery |
| JUG | Jugular vein |
| RJUG | Right jugular vein |
| CC | Co-registered MALDI-MSI dataset |
| DFM | Deep female mouse sample identifier |
| pos | Positive ion mode |
| neg | Negative ion mode |
| MSI | Mass spectrometry imaging |
| MALDI | Matrix-assisted laser desorption/ionization |
| LC-MS | Liquid chromatography-mass spectrometry |
File Descriptions
1. Ultrasound Measurements
C57_Female_US_measurements.xlsx
Contains ultrasound-derived vascular measurements for each mouse.
Variables include:
- Animal_ID: unique animal identifier
- Age: age of the mouse
- Body_Weight: body weight of the mouse
- Vessel
- Diameter_Diastole
- Diameter_Systole
- PSV
- EDV
- Mean_Velocity
- Flow
- Flow_Normalized
- WSS
- PI
- CCS
- Compliance
- Distensibility
2. MALDI Mass Spectrometry Imaging
The MALDI-MSI datasets are provided in the open imzML format.
Each .imzML file must be used together with its corresponding .ibd file, which contains the spectral data.
Brain
- cc_c57_brain_yfm_ofm_young_neg_60.imzML
- cc_c57_brains_yfm_ofm_old_neg_60micron.imzML
- cc_c57_brains_yfm_ofm_old_pos_60micron.imzML
- cc_c57_brains_yfm_ofm_pos_60micron.imzML
- cc_c57_brains_yfm_ofm_young_pos_60micron.imzML
Jugular Vein
- cc_c57_rjug_dfm_yfm_pos_10micron.imzML
- cc_jug_c57_yfm_ofm_neg_10micron.imzML
Carotid Artery
- cc_r_car_c57_yfm_dfm_3_5_10micron_neg.imzML
- cc_r_car_c57_yfm_ofm_4_8_10micron_neg.imzML
Typical MSI variables include:
- m/z
- Intensity
- TIC-normalized intensity
- Pixel X and Y coordinates
- Anatomical region
- Lipid annotation (when available)
3. Nikon Microscopy Files (.nd2)
The .nd2 files are raw fluorescence microscopy images acquired using Nikon NIS-Elements.
Examples include:
- OFM_C57_RJUG_section_1.nd2
- OFM_C57_RJUG_section_2.nd2
- OFM_C57_RJUG_section_3.nd2
- OFM_C57_RJUG_section_4_(1).nd2
- OFM_C57_RJUG_section_5.nd2
- YFM_C57_RJUG_4_section_1.nd2
- YFM_C57_RJUG_4_section_2.nd2
- YFM_C57_RJUG_4_section_3.nd2
- YFM_C57_RJUG_4_section_4.nd2
- YFM_C57_RJUG_4_section_5.nd2
Metadata stored within these files include image dimensions, pixel size, acquisition settings, fluorescence channels, and microscope metadata.
4. Histology and Fluorescence Images (.tif)
The TIFF images contain fluorescence microscopy and histological images of carotid artery and jugular vein tissue sections.
Naming Convention
| Suffix | Description |
|---|---|
| ch00 | Fluorescence channel 0 |
| ch01 | Fluorescence channel 1 |
| overlay | Merged fluorescence channels |
| top, bottom, left, right, lower, below | Cropped regions of interest |
| 20x | Image acquired using a 20× objective |
Files beginning with:
- OFM_CAR
- YFM_CAR
represent carotid artery images.
Files beginning with:
- OFM_Jug
- YFM_Jug
represent jugular vein images.
Channel-specific exports (_ch00, _ch01) contain individual fluorescence channels, while _overlay files contain merged channel images used for visualization.
Lipid Abbreviations
| Abbreviation | Full Name |
|---|---|
| AHexCer | Acylhexosylceramide |
| HexCer | Hexosylceramide |
| SHexCer | Sulfatide hexosylceramide |
| NAE | N-acylethanolamine |
| PC | Phosphatidylcholine |
| PE | Phosphatidylethanolamine |
| PI | Phosphatidylinositol |
| PS | Phosphatidylserine |
| PA | Phosphatidic acid |
| PG | Phosphatidylglycerol |
| CL | Cardiolipin |
| DG | Diacylglycerol |
| TG | Triacylglycerol |
| LPE | Lysophosphatidylethanolamine |
| MGDG | Monogalactosyldiacylglycerol |
| SMGDG | Sulfoquinovosyldiacylglycerol |
Missing Values
| Representation | Meaning |
|---|---|
| Blank cell | Measurement not available |
| NA | Not applicable or not measured |
| ND | Not detected |
Software Requirements
| File Type | Software |
|---|---|
.xlsx |
Microsoft Excel, LibreOffice Calc, R, or Python |
.imzML + .ibd |
SCiLS Lab, MSiReader, Cardinal (R), pyimzML (Python), or METASPACE |
.nd2 |
Fiji/ImageJ with Bio-Formats or Nikon NIS-Elements |
.tif |
Fiji/ImageJ, ImageJ, QuPath, CellProfiler, or other TIFF-compatible image software |
The MALDI-MSI datasets are distributed in the open imzML format to facilitate reuse without requiring proprietary project files. Each .imzML file must be accompanied by its corresponding .ibd file.
Software Used to Generate the Data
- Vevo LAB 10.0.0 – Ultrasound analysis
- SCiLS Lab 2026b – MALDI-MSI processing and visualization
- HDI (High Definition Imaging) – MSI data processing
- Fiji/ImageJ (v1.54) – Histological image analysis
- Bio-Formats (v8.5.0) – Import of Nikon
.nd2files - Nikon NIS-Elements (v7.01.00) – Microscopy image acquisition
- MetaboAnalyst 5.0 – Lipidomics analysis
- JMP Pro 17 – Statistical analysis
- Python – Data processing, visualization, and correlation analysis
