Eric Hoffman – Mouse Lung Scan


Google Presentation


3D Sectional View

3d section view from Web Master on Vimeo.

A multiplanar view reveals the bronchial passages and heart chambers in this set of mouse lungs.

Bronchial Passages View

bronchial passages from Web Master on Vimeo.

This video shows the bronchial passages in the mouse lungs after they have been highlighted by a filter.

Mouse Lungs Organic Shading

lungs 3d from Web Master on Vimeo.

This video gives an example of using the organic shading feature on the 3D viewer.

Axial Movie of Lungs

topdown movie lungs from Web Master on Vimeo.

An axial movie of the lungs’ CT slices. Note that the lungs were mounted upside down in the machine.



Scanner Settings
Machine Xradia microXCT
Source Setting
40 kV 200 µa
Source Distance
50 mm
Detector Distance 64.4mm
Pixel Size
11.9185 µm
FOV 24.41 mm
Magnification .495 X
Exposure Time 2 s
Image Size 2048 X 2048
Number of Projections 1648




The purpose of this scan was to better understand the structure of the Acinus of murine lungs and to provide a comprehensive and quantitative analysis of the respiratory system at the alveolar level. Another aspect is to provide data for stereological analysis and collect measurements of such parameters as density, parenchymal fraction and alveolar count. Because the scan was nondestructive, further study of the lungs is possible.


The subject of the scan is a set of mouse lungs that have been inflated and fixated to preserve the lungs in their inflated state. The scan is part of the wider study to provide a complete atlas of the respiratory system in mice and provides an elegant technique to study the smaller airways and respiratory structures without needing to resort to morphology and allows the non destructive study of murine lungs.

About the Scan

Each lung specimen is prepared using a similar protocol. The lungs are initially scanned in-vivo at different pressures. The lungs are fixed through perfusion using a modified Heitzman solution at 20cm pressure, following an initial pre-flush. The lungs are air-dried at 20cm pressure, 37 c temperature for 3 days and are scanned periodically to ensure preservation of shape and volume.Each LFOV scan is performed as the first step in identifying acinar locations for high resolution imaging. The settings for the LFOV scan are chosen such that identification of probable locations of acinii is possible by visually inspecting images. Magnification and image quality at that level of magnification is the deciding factor in setting parameters. The high resolution scans are conducted on the specific locations and the parameters are now decided by using not only image quality as a factor, but also the FOV to assure that an acinus is completely captured in the scan. The clear demarcation of alveolar walls is a necessity for analysis and the settings are chosen such that the resolution of the images is sufficient to capture the edge details accurately.

Links and Literature

Lung Assessment standards: 

Stereology and Morphometry: