At one time alchemy was generally regarded as being a dead-end pseudo science which was obsessed with transmuting base metals into gold. The modern rational science of chemistry evolved out of the muddled thinking of the alchemists, which is of no further relevance.
However, a modern re-evaluation of alchemy by Jungian psychologists has shown that much alchemical work was actually ritual intended primarily to bring about spiritual realisations in the mind of the alchemist, rather than changes in the states of matter, which were symbolic aids to visualisations:
'Carl Jung reexamined alchemical symbolism and theory and began to show the inner meaning of alchemical work as a spiritual path.
[...] The practice of Alchemy seemed to change the mind and spirit of the Alchemist.
[...] Organic and inorganic chemical substances, physical states, and molecular material processes as mere metaphors for spiritual entities, spiritual states and ultimately, transformations. In this sense, the literal meanings of 'Alchemical Formulas' were a blind, hiding their true spiritual philosophy, which being at odds with the Medieval Christian Church was a necessity that could have otherwise led them to the "stake and rack" of the Inquisition under charges of heresy. Thus, both the transmutation of common metals into gold and the universal panacea symbolized evolution from an imperfect, diseased, corruptible and ephemeral state towards a perfect, healthy, incorruptible and everlasting state; and the philosopher's stone then represented a mystic key that would make this evolution possible. Applied to the alchemist himself, the twin goal symbolized his evolution from ignorance to enlightenment, and the stone represented a hidden spiritual truth or power that would lead to that goal' - Wiki
So behind the facade of attempting transmuting physical substances, the alchemists were really transmuting mental qualia.
Presumably, by claiming that they were actually doing something 'practical' like transmuting lead to gold they could hide their true intentions and thus avoid charges of heresy and the attentions of the Inquisition. Alchemical symbolism and visualizations provided vivid and immediate analogies to 'external' operations in familiar artisanal processes such as brewing, smelting, churning, rendering, herbal extraction, distilling etc to bring about transmutations of 'internal' mental qualities.
Alchemical Visualization in Tantric Buddhism
The visualized 'cauldron' or vessel of transformation is a skullcup, known as a kapala in Sanskrit. Impure substances symbolising mental afflictions are transmuted to pure nectar of enlightenment by the power of a fierce wind-blown fire, with the reaction being 'catalysed' by seed letters.
Kapala (from Nepalese and Tibetan Arts Blog)
In a typical visualisation, urine, feces, brain/marrow, semen, blood and the meats of five taboo animals are transmuted into nectar
"When engaging in the generation stage practices one starts with the dissolution of everything into emptiness by reciting the mantra. This is done in order to eliminate self-grasping. From within emptiness the syllable YAM in a crescent moon arises, symbolizing wind. Then the syllable RAM in a triangle arises above it, symbolizing fire. Then from the syllable KAM arises a tripod of skulls. The skull which is the cauldron sits on the tripod. It is white on the outside and red on the inside. It is vast. In the center one pours urine in the form of the syllable HUNG. On the east one puts feces in the form of the syllable OM. In the north one puts brain in the form of the syllable KAM. In the west one puts semen in the syllable ANG. In the south one puts blood in the form of the syllable TRAM.
Then one puts fire in the form of HUNG. In the center of the five nectars one places human flesh in the form of the syllable HUNG. In the southeast corner one puts cow meat in the form of the syllable LAM. In the southwest one places dog meat in the form of the syllable MAM. In the northwest one places elephant meat in the form of the syllable HAM. In the northeast one puts horse meat in the form of the syllable TAM. The wind swirls around, generating fire out of the syllable RAM. This boils the substances in the skull cup, melting the five meats and nectars. As they boil, their color becomes orange red like the rays of the rising sun. The mandala of the moon is placed as a lid on the skull. On top of it are a white OM, a red AH, and a blue HUNG. Light rays radiate from the three syllables in the ten directions, reaching the Buddhas and bodhisattvas whose wisdom nectars are drawn back and dissolve into the vessels. The wisdom and samaya nectars become one and become white in color, cool in temperature, sweet in taste, and abundant in power. This becomes the collection of wealth and riches." - Tsok Practice
The urine, excrement, brain, sperm and blood represent the five contaminated aggregates to be purified. They are form, feeling, perception, karmic impulses and consciousness. The five meats symbolise the five delusions, which are confusion , miserliness, attachment, jealousy and self-grasping.
Another visualisation is the Kawang practice:
"At the heart of a Protector kangsol or puja, lies the recitation of the kawang otherwise known as kangshak, which literally means the ‘clearing of obstacles’. This is a special confessional prayer which is based on tantric visualizations, the recitation of which is to purify what may be significant accumulated negative karma threatening to obstruct one’s practice. Therefore, corresponding to the amount of obstacles that need to be removed, the actual visualization becomes particularly graphic. However, one should dwell on its true and subtle meaning and not on its apparently aggressive language that appears vicious, until the meanings are revealed. It follows that if the negative karma that blocks one’s practice is forceful, then the puja to counter it has to be equally intense.
The practitioner approaches the recitation of the kawang by visualizing the Three Poisons – Ignorance, Hatred and Desire which altogether encompass a myriad of other poisons such as delusions, negative karma, habituations and so forth. These negative elements are visualized in the form of a very large man or a woman. Then as the visualization continues, a dakini who is an emanation of Vajrayogini appears and she wields a cemetery chopper to slay that being who is the personification of our negativities. Then, she takes her chopper and slices the body in such a way that uncovers the inner organs.
First, she drains the blood into an offering vessel. Then, she cuts out the organs of the five senses – the tongue, nose, ears, eyes and heart and arranges them neatly into a skullcup thus resembling a grisly floral arrangement. Then, she pulls the bones out, arranges them into a vessel and burns the bones like stacks of incense sticks. Next, she extracts the human fat from the corpse and pours it into bowl, inserts a wick made of the human hair and lights it. Then she collects the rest of the bodily fluids like the bile, urine and so forth into an offering vessel. Then, she chops the flesh and mixes it with barley flour and places it into another vessel as food. Finally, she pulls the thighbones, cleans it and fashions it into a trumpet before placing it into a vessel as well.
While appearing grotesque at first, this part of the visualization is indeed a beautiful and meaningful gesture of transforming what is foul and turning them into sublime offerings. The blood represents the Water offering, the arrangement of sense organs represent the Flower offering, the crushed bones represent the Incense offering, the human fat set alight represents the Light offering, the bile and urine are transformed to represent the Perfume offering, the human flesh becomes the Food offering and finally the thigh bone becomes a trumpet to represent the Music offering...." Full article
RESOURCES FOR SYMBOLISM
C J Jung, Buddhism, Tantra and Alchemy
Numinous Symbolism - Pagan, Buddhist and Christian
Celtic and Buddhist symbolism - triskelions
Qualia - Objective versus Subjective Experience
Buddhism, Shamanism and the use of Psychedelics
Why Beauty Matters - Spiritual Art versus the Cult of Ugliness