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Interactive 3D Mouse Limb Anatomy Atlas

How the Atlas was generated

The Limb Anatomy Atlas was generated using embryonic mouse forelimb and hindlimb specimens stained using immunohistochemistry to detect muscle and tendon. Limbs were scanned using Optical Projection Tomography (OPT), reconstructed in 3D, and annotated using Amira 3D Visualisation software . The annotated 2D and 3D datasets are visualised using JAtlas Viewer software. High resolution 2D images were generated by High Resolution Episcopic Microscopy (HREM). The high - resolution 2D image stack is viewed using the JavaScript image viewer browser.

Materials

Forelimbs and hindlimbs were used from the Scleraxis-GFP tendon reporter line (C57Bl6 background) generated by Ronen Schweitzer (De Laurier, et al, 2006 - see references). Embryos were embryonic stage (E) 14.5 days gestation. Staging was based on criteria by Kaufman, 2001 (see references. Limbs were stained using immunohistochemistry to detect muscle and tendon (see Staining protocol in Downloads section).

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360° scan of hindlimb showing muscle stained using My32-Texas Red (red) and tendon (Scx-gfp) stained with GFP-Alexa 488 (green) antibodies

Optical Projection Tomography (OPT) scan and 3D reconstruction

Stained limbs were scanned in 360 ° using OPT microscopy. Scan data was then used to generate a 3D volume using back-projection reconstruction. Further information on OPT can be found on James Sharpe's OPT microscopy pages.

XY section reconstruction from OPT scan

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XY section reconstruction from OPT scan.

3D Rendering and Segmentation

Reconstructed datasets were visualised using Amira 3D Visualisation software. Individual muscles, tendons, and bones were defined using the segmentation editor of Amira, and saved as unique fields.