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This wiki page is a compilation of messages about cleaning diatom samples to remove organic contents of frustules and to separate the valves. The number with the message is the message number on the Forum.

Anne Gleich


I think it just the availibility what people are using, Bichromate or Permangant or HNO3. I prefer as you the Permanganat. It is not neccessary to handle Bichromat and not necessary to produce nitrous gases with HNO3. And yes I agree it is the experience to find for each sample another special protocol. 
Bu the basic steps are the same, and it is no mistake to start teh protocoll and to do a decision after each step.
For example, I had  sample which was complete clean after the HCl step!
Every (fossil) sample is a new adventure, and I have samples I really hate.


this is a good idea. Bu the problem is to split the valves, this is only possible with the hard acid method.

Bill Dailey

Diatomite Cleaning

Cleaning Oamaru Diatomite


Cleaning Oamaru Diatomite according to A.J. Doig

Excerpted and paraphrased by Bill Dailey from an article by Doig in the New Zealand Geological Survey Paleontology Bulletin 64.

About 200 cm3 of solid Oamaru diatomite is broken into pea-sized pieces and placed into an enamel-ware container. An equal or slightly greater quantity of sodium acetate is added and the container is heated on a water-bath until the sodium acetate melts completely. The container is removed from the heat and allowed to cool. A single crystal of sodium acetate is added resulting in the instant crystallization of the contents of the container with generation of heat. The container is left for an hour or two. It is resubjected to the boiling water bath, melted and the process repeated until the diatomite is completely turned into mud. After the final melting the slurry is poured into a 1-liter beaker which is then topped up with water. After being allowed to settle for at least an hour, the water is decanted and replaced. This is repeated about 8 times.

            Next the sample is treated with dilute hydrochloric acid until effervescence ceases. (Doig recommends not heating the solution since he says that sometimes heating will etch the forms.) After being left for an hour or more, the acid is removed by repeated changes of water.

            The slurry is added to an enamelled pot along with 1 liter of water and 1 tablespoon of Castile soap such as Lux. This is brought to a boil and allowed to boil for 30 minutes. It is returned to the beaker and the soap removed by repeated changes of hot water. A proportion of the earthy matter which remains in suspension in the soapy water is removed in the process. When the soap is almost completely removed the sample is returned to the pot, brought to the boil, and half a teaspoonful of bicarbonate of soda is added, very slowly, to prevent excessive frothing. After being boiled for about 20 minutes the sample is washed as before by successive changes of hot water, and more earthy material removed. With some resistant samples this process may have to be repeated two or three times.

            When all the soap and soda has been removed the sample is transferred to a Pyrex beaker and an equal quantity of concentrated sulfuric acid is added. The sample is then brought to the boil on a hotplate in a well-ventilated position where the acid fumes can escape, and the boiling is continued until the beaker fills with white fumes. If required the material can be bleached by the addition of small quantities of potassium chlorate. After being allowed to cool, the acid is removed by repeated changes of water.

            The soap and soda treatment is repeated several times until all traces of earthy matter are removed. A spread of properly cleaned diatomite should contain sand, diatoms, sponge spicules, radiolaria, and nothing else. There will be some large sand grains present and these are removed as follows: the material is whirled in a beaker, causing the sand grains to collect in a heap in the centre. The water containing the suspended diatoms is decanted. Repeated whirlings will remove all the diatoms from the sand, and with care, no diatoms will be lost. Fine sand is removed by passing the material through a 300 mesh sieve, which retains diatoms of 30 microns and larger. The sievings are not discarded, as a small number of diatoms of less than 30 microns diameter pass through.

Post-cleaning of Diatomite

Post-cleaning of Diatomite using Detergent
From an online article by Bill Dailey written before 2019. Not posted as a message. Lightly edited by Rob Kimmich.

After all the acids and oxidizers from cleaning are well washed out of the mixture, I add some water and some Sparkleen 1 detergent. I figure it’s like washing the dishes.

Washing. Add some water and some Sparkleen detergent. Use 0.5 teaspoon in 500 mL of sample. Avoid using very concentrated solutions since Sparkleen does contain base and this might damage the frustules. Carefully heat to a gentle simmer and keep it there for 30 minutes to a couple hours.

Rinsing. After it simmers, add water and let sit covered for an hour or more depending on the settling rate. Carefully decant. Repeat the wash, wait, decant at least twice more or until the water is no longer cloudy after the settling time. Check the sample under the scope.

Repeat the washing and rinsing with fresh Sparkleen several more times. Repeat this until clean forms are in the sample. One sample required 4 treatments. At the end you can tell things are working nicely by swirling the cooled beaker of sample on the table. If many clean sand grains congregate in the center, things are going well.

After the needed rounds of the process are completed, swirl the flask carefully on the table in a circular motion. This puts lots of clean sand grains into the center of the beaker. This is a good sign that the diatom forms are being cleaned. Go to the final stage of separating all the rocks, sand grains, and junk from the diatom forms.

The order of panning and sieving, and size of sieves which are used depends on the sample and the final sample requirements. Usually good to use a combination of sieves of various kinds and dishes to "pan". A squirt bottle of water is also very useful. The plastic sieves I use are made from nylon mesh of various sizes fused onto polycarbonate tubing or, in the case of a 72-mesh sieve, a big pill bottle with the bottom cut off.

General Cleaning


Bill, thanks for posting the link to the methods paper from South Africa. Lots of interesting information - watch for hippopotami while collecting, try potassium permanganate and HCl for cleaning, use ammonium chloride to reduce clumping. Things to try.

Craig Downing


My usual process is boil with HCl first, wash a few times, then H2SO4 with a few drops of saturated soln permanganate, boil to fuming. Then add 35% H2O2 (when cool!) to add about up to 1/3rd of volume to make piranha soln.and get rid of any organic matter left. Works well with many of my local samples which tend to have silt and/or much organic matter which may remain after the first step as carbon which the piranha get rids of easily. I don't have to think about it too much, just go through the process over a few days when I have time and end up with nice white cleaned samples ready for washing, sieving, panning etc.. This is all very nasty, dangerous stuff, and must be done with plenty of safety precautions of course.

Fortunately, I can get concentrated H2SO4 in Canada as drain cleaner which has organic additives fairly easily removed by adding H2O2. Alternatively, I have made some ~90% H2SO4 by boiling down battery acid on a hotplate down to fuming. Vendors of consumer lead acid batteries often fill up those smaller batteries for marine and lawnmowers etc. from a bulk supply and don't need the packs of acid that they come with. I called one locally and they were happy to give me a couple of litres worth of these acid packs for a very small fee!


One thing I have learned over the few years I have been cleaning diatom samples is to wash with water many times thoroughly decanting off between stages. Patience every step of the way - and a slow centrifuge helps! I usually run cleaned samples through a stack of plastic beakers with different mesh sieves in a cut-out bottom, sometimes 80-100 mesh, 60 micron, 20 micron and a 10 micron to sort by size and wash many times through passing the sieves, then decanting and if needed some panning in a small plastic dish to sort out heavy silt. A lot of clean small forms get caught in the 10u nylon mesh while passing fine silt.


I still find that using H2S04 with permanganate (either cold over a longer period as Klaus mentioned, or boiling it) is the most convenient for me. If the sample is cleaned well, I'll stop there and wash. If samples are with lots of organic matter, I'll boil off the water, then when cool add about 20% of volume of 35% H2O2 I keep cool in the fridge which seems to work even with very dirty samples (so a brute force method I suppose!).


I do all this processing outside in a box with a safety shield to house the hotplate, with protective gear for hands and eye/face... this is nasty stuff to be respected. I still process beforehand in HCl and a few washesto dissolve any salts that many precipitate in H2SO4, plus break up my samples - the latest of which are dried up samples I took from a salt marsh. Adding HCl to piranha would be dangerous, I have no intention of trying it!


Just a note on centrifuges and diatom cleaning. You don't need a centrifuge, but it can definitely save some time. If you do use a centrifuge it is better to run slowly. Spinning a tube to massive G forces will tend to smash delicate diatoms. Samples being washed can sit in a beaker for a few hours before decanting, which may not matter much if you are willing to take a few days through many washings, etc. during which you get on with your life. I find, like with most things related to diatoms, patience gives better results. I picked up a bulky lab surplus centrifuge, very cheap which I use with a few 50ml sample tubes and only spin it at a couple of hundred RPM for say 30minutes. Having the ability to hold larger tubes and even beakers is nice. That means I can do five or more washings in an evening while having dinner, doing work, watching TV or whatever, and be ready to let samples sit overnight, then pick up in the morning. Before I got my hands on this device I rigged up the rotor and tubes from a hand-cranked centrifuge to a geared motor to run at about 300 RPM.

Having a high-speed centrifuge is really useful for other things if you are getting involved with other aspects of this pursuit. I make my own styrax for diatom mounting by exposing raw resin to UV for weeks, then scraping it up and dissolving in toluene, and by then it is contaminated with dust and flies. Easiest way to clean it I find is to put in the centrifuge and run it as fast as it will spin (a couple of thousand RPM in my case) for a good while. After that the decanted resin is very clean.

Klaus Kemp


Thank you very much for this technique. I have taken the liberty of breaking your original into paragraphs and doing some light edits.


Alternative cleaning [from Klaus Kemp],

Having watched the recent exchanges caused me to rteflect back to a method advocated by N. I. Hendey, and if I am not mistaken he documented this in Diatoms of British Coastal Waters. This was using what has been termed as the "Cold Acid Method, the technique still uses the Conc. Sulphuric Acid but is never heated to the fuming stage. You will still need to do this in the open garden or ventilated area.

In a beaker add your sample of Diatoms, gently pour the sulphuric acid into the beaker, best done with small amounts at a time as there will be some heat generated at this point if water is present.

Make up a solution of Potassium Permanganate. Try to get it to the saturated solution point.

With a glass pipette, add a small amount into the beaker with the sample, this may create some frothing of the sample. Allow this to stand for an hour before adding further amounts of the Pot permanganate. As you add more and more of the Pot. Permanganate you should start to see a colour change, but as long as there no evidence of purple changing to pink and then white you will need to add more Pot. permanganate.

When the acid remains clear add the last lot of Pot. permanganate. There should now be no further reaction as all the organic matter will have been oxidised.

Leave the sample somewhere safe and out of the way from anybody or any animals which could accidentally knock over the beaker.

Next day gently add water to what should look to be a white residue, repeat adding and decanting the water till all traces of the acid have gone. I am fortunate to have a garden where I built a stone shed, knowing that I would be cleaning a lot of samples and I can with little chance of upsetting neighbours or enevlope them with acid fumes. I believe this is by far the preferred method for me, giving me excellent results from cleaning the most delicate forms to cleaning fossil deposit material.

I do not have to hand the Hendey paper but will send an update ASAP. Hope this of some help to those who need to avoid neighbours. You are encouraged to take all care when handling Acids and the onus is on you to practice this technique with safety in mind.

Raymond Hummelink


A friend of mine produces excellent strews with the hydrogen peroxide / potassium permanganate method. Often the strews are so clean that one would think he uses the hot acid method. This is what he does:

Add HCl 30% to the sample (same volume as the sample); wait for 2 hrs under occasional shaking/swirling;

Change water/rinse 4 to 5 times to remove HCl;

Add H2O2 (twice the volume of the sample). Heat to boiling, let it gently boil for 2 to 3 hrs;

Add a saturated solution (in water) of KMnO4; one drop at a time. Continue until the reaction has stopped. The sample is quite brown in color;

Add a milliliter or so of HCl, and then an equal amount of H2O2. This removes the brown.

After this the usual washings.

Rene Van Wezel


the addition of HCl to H2O2 doens't seem to generate nasty stuff (Cl2), but it catalyzes the breakdown of H2O2. So the samples do not clean very well.

Rob Kimmich

Here are some cleaning procedures published on Diatoms of North America. They give an insight into some ways the pros do it.