This article tries to provide a brief explanation of the meaning of Jing (精), Qi (氣), and Shen (神) which are known as the Three Treasures (三寶) of Chinese Qigong.
Jing refers to the Essence, or the material substance, from which life is formed. There are two kinds of Jing: Original Jing (元精) is the original essence or material substance that a new born baby inherits from the parents. After birth, the baby (and all the way to adulthood and later death) gets additional Jing, called Postnatal Jing (後天之精), from the food and air taken in by the baby (and later child and adult).
Qi refers to the energy that uses the material substance or Jing to build life as manifested via our human activities, like our motions and our thoughts.
Shen (神) refers to spirit, or the conscious and subconscious mind. This is applicable to humans and the animal kingdom. The plant kingdom does not have Shen. Therefore, Shen is the most important distinguishing feature between various types of living things; it is what makes an animal different from a tree. Shen directs and controls our activities, so that they are not just spontaneous reactions to external stimuli.
One can use the following analogy of a factory to understand Jing, Qi, and Shen. 
A factory has many raw materials (e.g., coal, metal, wood, oil) and machines (e.g., computers, hydraulic lifts and presses, assembly lines, trucks). The machines need power or energy to operate to produce useful products. For example, there are machines that can transform various raw materials into other machines. These other machines can use the raw materials to make other products for the factory to use or sell. The factory are run and operated following certain rules, processes, and management governance.
Jing, the Essence or the material substance that we inherited at birth or acquired in life, is like the raw materials in the factory from which products are made. Qi is like the energy that powers the machines. Shen, the spirit or the conscious and subconscious mind, is like the rules, processes, and management governance that direct and run the factory. In Qigong, Jing is the raw material from which life is made. Qi is the energy that powers the making of life. Shen is the conscious and subconscious mind that directs and controls that production process (for example, the brain stem controlling the heart rate, respiration, etc.).
In Qigong and Traditional Chinese Medicine (TCM), Jing, both the Original Jing and the Postnatal Qing, is stored in the kidneys (腎). Qi that is used to make life from Jing is stored in the Lower Dan Tian (下丹田), an area a couple of inches below the navel and a couple of inches inside the body. Shen is stored in the Upper Dan Tian (上丹田), an area in the brain behind the spot between the eyes.
In Chinese, there are two words used to describe the mind: Xin (心) and Yi (意). However, their meanings are not identical. Xin means heart in Chinese and in Qigong it refers to the emotional mind. Yi is the mind that is related to wisdom and judgment. When a person’s Xin has an idea, it means that he is determined to follow up with that idea. When a person’s Yi has an idea, it means that he is formulating a method that can make that idea into reality. You want both the Xin and Yi behind an idea. Sometimes the emotional mind is stronger than the wisdom mind; then you may act according to how you feel, and not how you think.
To have good health, you need to have good Jing by eating healthy meals and have adequate sleep. You need Qi to power all your activities; so you need to practice Qigong to produce Qi from your Jing and to circulate your Qi to all parts of your body, including to the Upper Dan Tian to nourish Shen where it is stored. Since the mind is directly involved in practicing Qigong, Qigong practice, in addition to providing Qi, also cultivates and exercises Shen.
In physiology, we have various types of circulatory systems associated with the blood system, nervous system, and lymphatic system. In Qigong, there are supposed to be reservoirs to store Qi and a system of meridians to circulate Qi. How are these Qi reservoirs related to our known organs? How is the Qi circulatory system related to our known physiological circulatory systems? How are Qi and blood related? How much and which parts of the traditional Chinese explanation of Qigong will be verified in the future? These and many other questions are waiting for modern medical and scientific research to find out.
 I learned this analogy from the book The Root of Chinese Qigong: Secrets of Health, Longevity, and Enlightenment by Dr. Jwing-Ming Yang, 2nd edition, 1997.