Objective  To investigate the stereoscopic shapes

locations and relationships of substantia nigra

red nucleus

and the main related nuclei based on the cross-section images from the dataset of the first Chinese Digital Visible Female

and to reconstruct the 3-D model of the structures.   Methods  Extracted cross-sectional images of the substantia nigra

red nucleus and the main related nuclei were collected and investigated. Every construction was outlined respectively by using Adobe Photoshop. The 3-D reconstructions and visualizations of these constructions were realized by Amira software.   Results  The cranial end of substantia nigra and red nucleus were located at the continuum of the midbrain and diencephalon

closely related with the nuclei

the crus fibers

the optic tract

etc.

in the diencephalon. The substantia nigra run through the whole investigated area

and the caudal end disappeared nearby the superior border of the basilar part of pons. The height of red nucleus was about two thirds of the height of substantia nigra

and the caudal end disappeared gradually after entering the inferior colliculus. The 3-D model reconstructed by Amira software demonstrated clearly the shapes and spatial relationships of substantia nigra

red nucleus

main related nuclei in midbrain and the continuum of midbrain and diencephalon. The reconstructed model was rotated

cut

and recombined at any angle

and the relevant structures were displayed as a whole.   Conclusion  The shapes and locations of substantia nigra

red nucleus and their relationships with other nuclei are demonstrated clearly. A 3-D model is also reconstructed

which providing more ocular and convenient reference for anatomic study and clinic application.