How To Digitalize Natural Sciences Collections?



Scorpion pictured in UV fluorescence. Focus stacking image.
How To Digitalize Natural Sciences Collections?
post by
Siska Van Parys

Researchers from the Royal Belgian Institute of Natural Sciences and the AfricaMuseum have published a handbook on how to digitalize natural history collections. This can be done in fifty ways, and in fifty shades.

By digitalizing museum specimens in 2D and/or 3D and making them available online, they are accessible to researchers all over the world. Thanks to high-resolution images, the specimens often no longer have to leave the museum conservatory - with its ideal storage conditions - and are not damaged by manipulation and transport.

At the same time we prolong the 'life' of these collected animals, fossils or geological samples, when the physical object would have disappeared or destroyed. Just think of the millions of specimens that were lost forever in the fire at the National Museum of Brazil in Rio in 2018.

Tailor-made approach

Natural history specimens are pinned, placed on a microscope slide or stored in an ethanol solution. They are sometimes colourful, sometimes translucent, or very shiny. Capturing such diversity successfully is not a piece of cake. Each type of object requires a tailor-made approach.

“With this handbook we offer an overview of the possible ways to digitalize natural history specimens and heritage objects. We discuss the pros and cons of each technique, and for which type of object it is best suited,” says Jonathan Brecko (RBINS/AfricaMuseum).

“The manual is easily accessible and is also intended for readers without prior knowledge who want to start a digitalization project. We also describe costs and propose workflows that can help people in a very concrete way.”

Seeing through it

In addition, digital imaging allows researchers to collect new information about the specimen that cannot be obtained from the original. On a 3D model, for example, it is much easier to see the spatial structures and to calculate surfaces and thicknesses. “Such new research techniques were not possible with the 'real' objects,” explains Aurore Mathys (RBINS/AfricaMuseum). “Recently we discovered a rare snake inside another rare snake.”

“Another example is multispectral photography. We photograph under different wavelengths, for example with UV and infrared light”, explains Mathys. “This allows you to see things that are invisible under normal, white light, such as damaged parts, earlier restorations or the composition of the materials and layers of paint in the case of heritage objects.”


Many specimens from our collections - especially the type specimens (on which the description and name of a new species is based) - have already been brought to the lens by the digitization team. You can view them online at

The handbook itself is available free of charge and was published in the Collection Management series of the European Journal of Taxonomy, which is published by our Institute, among others.


These are the techniques that have been evaluated, perfected and compared:


  1.     Focus stacking
  2.     ZooSphere and DISC3D
  3.     RTI and Portable Light Dome
  4.     Structure from Motion
  5.     Structured Light Scanning
  6.     Laser Scanning
  7.     Infrared Depth Sensor
  8.     Multispectral imaging
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