Nuclear magnetic resonance imaging (MRI) is a technique to create a three-dimensional image of a fetus. Doctors often use MRIs to image a fetuses after an ultrasound has detected an, or has been inconclusive about an, abnormality. In 1983 researchers in Scotland first used MRI to visualize a fetus. MRIs showed a greater level of fetal detail than ultrasound images, and researchers recognized the relevance of this technique as a means to gather information about fetal development and growth. Researchers later used the technology to take measurements of the uterus, placenta, amniotic fluid, and fetus during the first trimester of pregnancy. MRI provided doctors with a non-invasive method to diagnose and treat fetal abnormalities and maternal conditions such as pre-eclampsia.

In March 1999 Bradley Richard Smith, a professor at the University of Michigan, unveiled the first digital magnetic resonance images of human embryos. In his article "Visualizing Human Embryos for Scientific American," Smith displayed three-dimensional images of embryos using combinations of Magnetic Resonance Microscopy (MRM), light microscopy, and various computer editing. He created virtual embryo models that it is possible to view as dissections, animations, or in their whole 3D form. Smith's images constitute a new way of visualizing embryos. They served to help students, researchers, clinicians and the general public interested in the study and investigation of human embryonic development.

Magnetic Resonance Microscopy (MRM) is an imaging method that allows the visualization of internal body structures. Using powerful magnets to send energy into cells, MRM picks up signals from inside a specimen and translates them into detailed computer images. MRM is a useful tool for scientists because of its ability to generate digital slices of scanned specimens that can be constructed into virtual 3D images without destroying the specimens. MRM has become an increasingly prevalent imaging technique in embryological studies. Through MRM, the first 3D human embryo images were created as part of the "Multi-Dimensional Human Embryo" project, a public database of three-dimensional embryo images.