A few tips for the preparation of objects

Our µCT works different than the CT’s used for human medicine. The scanned objects rotate around their own axis while detector and source are fixed. Torsten Brandmüller illustrated this method very well on Wikipedia:



Therefore, we need to ensure that our specimens don’t move at all! It is like taking a picture with a camera. Clicking the release while jiggling the camera results in a useless photograph. However, µCT scans take longer than photos and require elongated object stability. We devised different options for the preparation of our objects.




Simple preparation of recent material for scanning bones

The preparation of objects conserved in alcohol is more or less a big challenge. As already mentioned, the animals may not move during the scan. Furthermore, it’s important that the specimens don’t dry out or get any other damage.

A good way to reach high-quality scans is the use of slightly wetted foam material twisted around the specimen. You can also use completely closed vessels, consisting of different material and shapes, as you like… well, only ceramic and glas are no appropriate materials, due to their high reflection rate and density. In fact, plastic is best for the scan.


20150515_174038     20150515_174421     20150515_174019

If you have vessels without lid, no problem! A plastic tube closed with tape is enough to avoid evaporation of alcohol during the scan. Another idea is to put packaging material into the tube. This avoids movement and evaporation due to less air inside the tube.


Simple preparation of fossils and other hard material of common size

The preparation of fossils is easier than of recent material. Either we fix the specimen on top of a glass stick, or we put it in a plastic vessel.

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Fortunately, fossils don’t need to stay wet, so the way of preparation doesn’t matter. In case of specimens of similar size, it is worth it to make an all-purpose fixture. An example can be seen in picture two: cones of Styrodur. This material is firm but easy to cut (with a cutter knive). We found out that cone-shaped fixtures suits most of the objects and you can be very creative in size and choice of material.


Advanced stage: Preparation of micro specimens

A problem is that micro specimens are tiny and differ from each other.


As you can see, we first tried to make individual fixtures, but with putting the tiny specimen into it or at least with taking it out, it usually gets damaged. Mostly we scan fragile insects, chalk skeletons, and small vertebras. Two methods became very useful for this:

1.    If the object is tiny but robust, we prepare it in small ordinary „Eppis“ (Eppendorf tubes) used in every lab.



This method is very good for the fossil vertebras and single bones. To save preparation time we can put several pieces in one Eppi and make single scans of each specimen.

2.    In case the object is tiny and fragile I always ask my guest the question: „How valuable is the specimen for you?“. When there are more than one specimens, the best is to just glue it on a glass stick:




A hot glue gun is perfect for bigger insects. Nail polish works very well for tiny objects.



Both methods should be handled carefully, as even tiny marks on important parts of the object are visible in the scan and should be avoided. Glue and nail polish also affect the chitin of an insect, so it should only be used for body parts you don’t need for further purposes like the abdomen or the head.

You cannot use the glue-method, if you need the complete animal. In that case you must build a fixture as mentioned above.



For professionals: special cases

Hier sind ein paar wenige unser Spezialfälle aufgelistet, die hin und wieder mal reinkommen:

1.  What do I do with fossil plates?

It’s kind of a pain to prepare and scan fossil plates, as other technicians could tell you, too. They are very fragile, they doesn’t lay in the centre during the scan, and strong effects of an overexposure could occur, and so on and so on…

Adequate fixtures are made of material on front and back side. The plate should stick out on each site. This can be build by a technician (left picture) or you make it on your own using material of your choice (right picture):

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Basically, all the fixtures serve the purpose, but it’s important to have a look on two things: firstly, a stable base-plate is a must (different to that one on the right site of the right picture where no plate is present). Secondly, you need enough adhesive tape. Usually, we wrap the plates in a layer of bubble wrap, put it in the fixture and fix it with the tape. With this method specimens cannot drop out of the fixture. Anyway, if a fixture fails for whatever reason, the wrap finally protects the specimen.

2.    What do I do, when I’d like to scan stained musculature in its original position?

Staining with potassium iodide or Phosphotungstic acid is a great thing! We work with virtual illustration of soft tissue very often and therefore are confronted with the problem of how to prepare the animal without loosing its natural posture.

As mentioned above, when preparing recent material, the animal is put into a tube, what results in slightly squeezed pictures. When we analyse bones it doesn’t matter. But when analysing soft tissue, this method is hindering the illustration:


Bipes_Arme anliegend_Querschnitt     Bipes_Arme anliegend_3D_heller



Furthermore, skin crinkles from squeezing an cause a movement of the musculature. This inhibits an acceptable reconstruction. Well adapted fixtures for each specimen is a big help and could look like this:


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Although it is no natural position of a lizard, its arms lay stretched out on a plastic rack, as this is the easiest way to reconstruct the musculature afterwards. Also important is that the animal doesn’t dry out, so we put bubble wrap and tape around the lizard (see picture on the right).

The scans look much better now:


Meroles_Welle_2     Bipes_Arme ausgebreitet_Querschnitt     Bipes_Arme ausgebreitet_3D


3. What do I do with unhandy fossils?

If you have really and absolutely unhandy, heavy or fragile fossils, it is necessary to create further fixtures like plaster moulds, which can easily be stuck on a turn-tilt plate:

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Unfortunately, this is very time-consuming so we only do it for special specimens. It causes a mess, by the way, so the preparators help us out with this (thanks a lot to our colleagues!). For this reason you should make an appointment with us to discuss the preparation and a second one to scan your object.





This is it for now, but when I get new exciting pieces I will upload them, of course!

If you have any suggestions or questions just send me an email to mikroctlabor(at)mfn-berlin.de!