Things to keep in mind when ordering thin sections

When ordering thin sections it's a good idea to ask for:

  1. colored impregnation of the porosity
  2. a slightly too-thick section because this gives you flexibility to later choose to polish the section for electron microbeam work, or to polish off a bad staining job (or both) with less risk that your section will end up too thin.
  3. the cover slip to NOT be glued in place (most likely, you'd prefer to mount cover slips yourself, with an index medium).
  4. An exception to the slightly too-thick rule concerns very fine-grained rocks---for those a slightly thinner preparation may allow you to get more light through the specimen and see textures and fabrics that would otherwise be obscure.

Whether you wish to have the thin sections stained for mineral identification, and whether you wish to have this done by the thin section maker or to do it yourself, depends on many factors.  See the section on stains to explore this further.

The Importance of Having Colored Porosity

The invention of color impregnation media was one of the greatest technical advances ever made in sedimentary petrology (perhaps best after the invention of the thin section itself, and, maybe, in this writer's opinion, back-scattered electron imaging).  If you look at old petrology papers, from before the days of "colored epoxy", what you see is that nobody makes much mention of the porosity.  That's because they couldn't really see it well enough to appreciate it properly!  Because of the confusing visual field presented by plucked holes in the thin section (black under cross-polars, clear in plane light) and grains and crystals at extinction (black, clear), discrimination of the 'real' porosity (also black, clear) was pretty much, guess work.  And, of course, without a good view of the porosity, nobody could even think to talk sensibly about IGV (intergranular volume), at least not in compacted and cemented rocks.  Colored impregnation media changed all of this.  Suddenly people could see what was going on; they could discriminate primary from secondary from induced porosity.  In the late 1970s, there came a flood of papers describing  pore type variations and the IGV concept soon came into widespread use in sandstones and the complexity of pore systems in carbonate rocks gained heightened appreciation.

The way a colored impregnation medium works is this:  The small rock slab (a billet) that is about to become the thin section is submerged in a liquid impregnation medium. Today this medium is typically some sort of plastic resin [no longer "epoxy", though that remains a common term in the vernacular] dyed blue. Thesample is then pressurized to drive the colored medium into all the pores. Then the resin is cured. At this point all the natural pores of the rock are filled with solid blue stuff.  Next, the thin section is produced by slicing through the billet, giving the exposed surface a slight polish, and gluing it to the thin section glass with a clear resin.  The billet is cut from the glass, leaving only a thin slice that is then further thinned to the thickness of a standard thin section (30 microns).  If everything has worked well (alas, incomplete penetration of the blue resin is a common flaw in low-permeability rocks), natural pores will be filled with the blue resin whereas any holes created by plucking and gouging during the grinding and final polish of the section will be filled only with the clear resin.

Cover Slips

As mentioned in the introduction to this section, avoid having cover slips permanently affixed to your thin sections at the time they are made.  An exception: if the section is to be used for teaching purposes, year after year, with a rather large class; even then you might want to wait until after the section is stained.

That said, unless your thin section is polished for electron microscopy, working without a cover slip is unthinkable!  First of all, many microscope objectives are constructed assuming that a cover slip (typically, 0.17mm) is part of the optical system.  Second, and more noticeably, a cover slip allows you to place a uniform layer of index medium into the small roughness on the thin section surface, serving to reduce the contrasts in index (see discussion of crystal optics) at crystal edges.  There is less contrast between the edge of a crystal and the index medium than between the crystal and the air.  What this means is that with a cover slip and an index liquid, more of the transmitted light will make its way up the objective and to your eye, rather than being scattered to create confusion at every tiny scratch, pit, and crystal boundary.

Compare the two images below. The image on the left was made from a reasonably well-polished thin section without a coverslip, the image on the right made after the coverslip was applied:

applying a cover slip - step 1 applying a cover slip - step 1

How to Apply a Cover Slip

Here's how to apply a cover slip gracefully (i.e., without making a mess).  Start with a clean, dry thin section.  Icky finger prints will make the index liquid disperse unevenly.

applying a cover slip - step 1 1. Use a glass rod to place a small drop (diameter of a pencil eraser) in the middle of the thin section.
applying a cover slip - step 2 2. Take a clean cover slip and align it with the thin section, tilted over the drop.  Allow the cover slip to fall onto the drop.
applying a cover slip - step 3 3. Now apply light pressure in the center of the section with your fingernail (careful! No fingerprints!) or a pencil eraser until the liquid has spread about half-way to the edges of a section.  Over the next few minutes it will spread the rest of the way by itself.  If bubbles in the liquid seem annoying, you can chase them to the edges with light pressure from your fingernail or a small tool, as long as you don't press so hard you crack the cover slip.
applying a cover slip - step 4 4. If you used too much liquid, it may emerge in little drops around the edge of the cover glass.  These little drops can be carefully removed with a tissue.  Just don't smear the stuff into the middle of the cover slip!  Wipe away from the center of the slide.  If you have not applied too much liquid, and you handle the section carefully, by the edges, the cover slip should easily last for several months and will not leave a gooey mess in your thing section box.

Index Liquids

Suitable index liquids for applying cover sips include: water, actual index oil (n=1.465 is standard; these are expensive), mineral oil, and glycerin.  Water evaporates too quickly to be much use, except in a pinch, when it's better than no index medium at all.  Index oil can be obtained from suppliers of optical equipment but is relatively expensive, has a limited shelf life, and may have toxicity issues.  The final two can be obtained from ordinary retailers (drugstores). Mineral oil is longer-lasting, but requires strong detergent or organic solvents for removal; glycerin can be readily removed with water, but will evaporate from beneath the cover slip after a few months.  A caution: glycerin has a sweet taste and may attract scary-looking insects if you leave the lid off.

Staining

Staining, done properly, saves petrographers lots of time, though this is generally more true for the staining of feldspars in sandstones for purposes of point-counting, than it is for carbonate rocks. Stains can also increase the accuracy of petrographic determinations. Carbonate petrographers must accept that calcite versus dolomite is a determination that cannot be accomplished based on optical properties (relief and birefringence). Crystal shape and other context can provide powerful hints, but ultimately, one must turn to chemical or X-ray methods for certainty.

Stains commonly used for carbonates are as follows:

               stain                       calcite     dolomite    Fe-dolomite

            Alizarin red-S             pink         no stain      no stain

Potassium ferricyanide            no stain    no stain      blue

Lots of things can go wrong with a thin section stain. Too-aggressive etching can completely dissolve small crystals, especially if the thin section is too thin. For this reason, staining is never recommended for calcareous mudrocks, in which calcite crystals tend to be small, almost by definition. Also problematic is the fact that stains can soak into microporous rock components independent of their reaction with the material, giving a false impression of composition and also obscuring the nature of the microporous thing. The widespread use of electron microbeam imaging has greatly reduced the motivations for staining thin sections. If your study will have access to even a bit of data from back-scattered imaging, cathodoluminescence, EDS, or X-ray diffraction, then staining your beautiful thin sections is probably best avoided. Keep in mind that staining will ruin any polish (because of the etching) and make your samples unsuitable for probe analysis or any other electron beam method (because of the etching and the applied chemical coating). Stained sections that need to be examined by these methods will need to be re-polished (and hopefully, you asked for slightly thick sections so this will be possible).

Finally, there are schemes touted in the literature for using shades of mauve and purple to discern the relative Fe-content of calcite and also the intensity of blue to discern the relative Fe-content of dolomite. KLM's opinion is that such an approach is highly suspect because variations in stain intensity are controlled by so many variables unrelated to mineral composition. Careful testing of composition with the electron microprobe has demonstrated in many cases that stain color can be highly deceiving. The table given above is about as far as you can take it with regard to the accuracy and precision of mineral composition determined by staining. But if you're after just a hint on calcite composition:

               stain                       calcite     Fe-calcite   dolomite    Fe-dolomite

    Two stains combined          pink         mauve       no stain        blue

If staining fullfills some compelling research need (say, you need to determine dolomite abundance by point-counting), follow the recipes give here, on sections of correct thickness and reasonably good polish, and you probably won't come to grief. Remember the important option to only stain half of the section.

Chemicals:

Alizarin red-S. Dissolve 1 g of alizarin red-S in 500 ml of 0.2% HCl (2 ml of concentrated HCl in 998 ml of distilled water). Shelf life of several months.

Potassium ferricyanide. Dissolve 2.5 g of potassium ferricyanide in 500 ml of 0.2% HCl. Shelf life approximately 4 hours.

Given the contrast in shelf life, if you're mixing the stains, mix only a small volume---no need to pitch out a whole liter of Alizarin Red-S if you're only staining a few sections.

Etching solution. 2.0% HCl. (10 ml of concentrated HCl in 490 ml of distilled water).

Procedure:

Use clean, dry thin sections. Clamp two sections back to back with a test tube clamp (if you can find one) to speed things along. Make an assembly line of 5 beakers (250-500 ml) and use the following timing protocol:

1. Etch solution: 5 to 10 seconds

2. Potassium ferricyanide: 2 to 3 minutes (longer for coarser crystals)

3. Distilled water rinse.

4. Alizarin red-S: 20 to 30 seconds

5 Distilled water rinse.

Use a gentle rinsing action, drain water from slides, and air dry.

Stains can be mostly removed by vigorous washing of the section and can be completely removed by re-polishing. Stains may survive one coverslip replacement if you simply pull the coverslip off and replace the index medium without washing the section.