Chemical Reference

Many of the chemicals required in microscopy are easily obtainable, but the houses which would supply to a professional are frequently out of the price range of the amateur. When seeking out ones supplies from firms which do not specialize in the needs of the microscopist it’s vital to know what one needs. It’s hoped that the following provides something to those getting their start, be it an explination of antiquated terminology or an aid in determining suitability. I will update the list as my whims and time permit.

  • Alcohol: Anything from a glass of brandy to pure methyl alcohol. When a particular type (or concentration) of alcohol is called for it will likely be mentioned. Be aware of what the alcohol is required for, dehydration requires a very pure concentration as the last component of a series so use an alcohol that can be diluted to create the preliminary components of the series. As a solvent most alcohols will be effective to a similar degree but some are more prone to quality issues than others. Make an economically motivated decision for the alcohol used regularly and stick with one throughout the processing of a particular specimen. Do not drink the alcohol intended for microscopy even if it is from the liqueur store, accidents happen.
  • Benzene: The late great Benzene was the go-to solvent of choice for many microscopists. Extremely toxic and volatile it is largely unavailable and has been superseded by many other alternatives. Don’t go out and buy Benzene, get Xylene instead.
  • Canada Balsam: Also called Balsam, Canada Turpentine, or Balsam Fir Gum, it is the distilled resin of the Balsam Fir, Abies balsamea. This terpene was the primary resinous mountant for all optical applications. Used for mounting slides its characteristics are better known and documented than any other resin. It is rapidly soluble in many solvents, and resists crystallization for longer under more adverse conditions than many alternatives. It is often rather acid and may bleach stains where other mountants would not. Natural Balsam is generally preferable to that which has been purified and hardened prior to being liquefied by another solvent such as Xylene as natural Balsam is forgiving of imperfectly dehydrated specimens. It is the mountant I commend to all those starting out. Buy it from the hippies who think it’s medicine.
  • Clove Oil: An essential oil produced from various parts of the clove plant, Syzygium aromaticum. Oil may be produced from the plants buds, leaves, or stems. Bud oil is the most impure because of the likelihood of buds at different stages of development being processed together. Stem oil is often not strictly from the stem but rather the portion of the plant that remains after harvest. Leaf oil is the most reliable and widely available, it is well suited as a clearer for resinous mounts or as a slow acting solvent. Highly filtered variates were once recommended as immersion fluid. Clove oil is most economically obtained from companies that supply the makers of incense.
  • Denatured Alcohol: Ethanol plus some additive which renders it irretrievably unfit for human consumption, so that the taxes and restrictions on Ethanol do not apply. There are different means of denaturing alcohol and some are unsuitable for the microscopist. Denatured Alcohol which contains Xylene can not be effectively diluted for dehydrating in series, but is suitable for situations which call for anhydrous or 95% Ethanol. Alcohol denatured by the addition of Methanol or Isopropanol, alone or in conjunction is ideal. Do not use Denatured Alcohol which has been colored. Hardware stores will carry it in the paint aisle and the label should provide information as to the denaturant.
  • Essential Oil: An unrefined natural oil distilled from a plant source, see other entries for specifics. Today essential oils are complicated by the proliferation of homeopaths and aromatherapists who sell their own essential oils online. I can not recommend these sources as generally persons who accept homeopathy as a viable field are unable to observe effective protocols for production. There are exceptions but as a source quality is unreliable and if contacted will always be described as excellent by the producer. It is better to obtain essential oils from commercial rather than boutique suppliers.
  • Ethanol: Grain alcohol, no different from that in beer, wine or liqueur. Due to the fact it can be “safely” drunk it is regulated in many countries and may not be available for purchase by persons under a certain age, or above a particular concentration. It’s the most expensive option among the alcohols, but that most often used in scientific applications because it is the least toxic. The gold standard for dehydration is anhydrous ethanol. Everclear is the strongest Ethanol available at liquor stores in the United States. Some chemical supply houses will ship to private residences but it is rather more expensive. I’m told some schools will procure it inexpensively on their account for those willing to make demonstrations to the students.
  • Histo-Clear: Is a comparatively non-toxic solvent and clearing agent. It is miscible in many resinous mountants and I’m told not as harsh scent-wise as either Xylene or Benzene. This will only be available from sources dealing with microscopy and its attendant supplies.
  • Methanol: Wood alcohol, the stuff that will cause blindness if drunk in place of ethanol. More expensive than other options, it is superior because it may be obtained in high concentration at lower cost than ethanol in may countries. Occasionally a simple permit is required to authorize it’s purchase. Analogous to Ethanol for essentially all microscopical application except in the case of some stains. Stay away from colored Methanol. It can be found at some hardwares or as a specialty fuel for small engines etc.
  • Isopropanol: Rubbing, or isopropyl, alcohol is available nearly the world over without restriction. It is more expensive at the upper end of concentration but it can be easily reclaimed or purified from dilute solutions. It is toxic, but can be substituted for both Ethanol and Methanol in most situations without detriment. May be obtained at 70-90% from most groceries and pharmacies. The pure form is not uncommon at stores catering to farmers and others who may produce bio-diesel.
  • Pure Gum Spirit of Turpentine: Often called Spirit of Turpentine or simply Turpentine it is a resin of numerous species of the genus Pinus. An effective solvent and clearing agent, largely superseded by synthetic compounds it can still be very useful for some applications, notably as a clearer for situations requiring perfect dehydration. It is a less toxic alternative to Xylene but is not as effective as a solvent. Found at art stores and the paint aisle of hardware stores.
  • Toluene: Used in some techniques as a replacement for Benzene. Toluene is another formerly widely used solvent, though somewhat less volatile than Benzene. It is recommended for few uses as it has a tendency to result in the rapid (a matter of months or years) crystallization of mountants, though some authors lauded it. Don’t use Toluene.
  • Turpentine: Technically any of the volatile terpene group chemicals. In microscopy it will always be qualified in some way. See other entries; Venetian Turpentine, Pure Gum Spirit of Turpentine.
  • Venetian Turpentine: A resin of the western larch, Larix occidentalis. An expensive resinous mountant more often used as a component of other compounds than alone. Available from the finer sort of artist supply houses.
  • Water: Not all water is created equal. In microscopy one should take note if any text refers to water without any other description. For starters there’s: distilled, reverse osmosis, filtered, tap, bottled, pond, rain, hard, soft, neutral, and demineralized. If I say water I’ll do my best to specify. When it doubt, choose distilled.
  • Xylene: Xylene or Xylol is an effective solvent and clearing agent. Inexpensive and readily available it is a less toxic than Benzene and far less costly than Histo-Clear. Xylene will turn cloudy in the presence of water and is unsuitable for use on specimens which are not perfectly dehydrated. It is an effective and highly volatile solvent for use with most resinous mountants. The paint and solvent aisle of most hardwares will offer Xylene.


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