VIRMISCO — The Virtual Microscope Slide Collection

Digitisation – A virtual research infrastructure

Digitisation allows science rapid access to research objects while conserving the originals. The linkage of diverse online resources creates a virtual research infrastructure that provides completely novel opportunities for science.

To optimise their use in research and to ensure comparability, digitised materials should be produced under the same conditions (for instance with respect to resolution and colour fidelity). This requires the definition of precise standards for digitisation. For two-dimensional objects such as drawings, photographs, texts and prints, long-lasting experience and comprehensive standards already exist. For transparent to semitransparent three-dimensional microscopic objects, such as microinvertebrates or microscopic pieces of fungi, plants or other animals, the definition of standards is still in its initial stages.

The digitisation of three-dimensional microscopic objects

The digitisation of three-dimensional microscopic objects several techniques come into consideration: bright-field microscopy, laser confocal microscopy or nano-CT. We therefore chose the bright-field microscopy with best results achieved with differential interference contrast microscopy (DIC) producing stacks of optical sections (z-stacks). Furthermore, it is a technique which up to now is widely used and easy to realise. In this project we are developing standards and recommendations for taking microscopic image stacks of 3D objects.

Recommendations for digitisation

We therefore recommend as a standard for the digitisation of three-dimensional objects as permanent preparation of soil organisms : (1) series of photographs with different focal planes (z stack); (2) using a microscope with motor focus; (3) at least one photograph with scale bar and measure of length; (4) bright-field microscopy, especially differential interference contrast microscopy (DIC); (5) the following metadata should be documented: creator of photographs, creation date, producer / type of microscope, producer / type of camera.

From images to a virtual microscope

The transfer and presentation of large data volumes which rapidly arise by z-stacks in high quality via the internet is a challenge. We use compression techniques in order to maintain image quality as far as possible. The original tiff files are converted to jpeg and then converted to a Theora / Ogg compressed video file. The „video“ can be viewed in the online VIRMISCO viewer, which enables the user to focus online through the object as if using a real microscope. Additionally, the viewer offers features such as rotating, zooming, and measuring, changing brightness or contrast as well as downloading complete z-stacks as jpeg files or video file.

The benefits of VIRMISCO

Virtual access to collections for taxonomic studies, like type material: Loans might become obsolete and prevents material – especially old and fragile one – from damage and loss. The object can be digitally conserved and restudied anytime, anywhere again, irrespective of completeness and quality of the descriptions and figures available on this material or loss of the original material.

New way for taxonomic publishing: Instead of producing drawings, which is very time consuming, the deposition of z-stacks in VIRMISCO in addition to the description and sketches or drawings will be a more realistic and objective documentation of the studied objects.

Education and taxonomic training since it constitutes a virtual reference collection.

Statistics: VIRMISCO provides more then 4700 image stacks; Acari (Gamasina: 215 Individuals (87 taxa and 198 types); Uropodina: 116 Individuals (34 taxa and 116 types), Oribatida: 15 Individuals (5 taxa and 1 type)), Collembola: 58 Individuals (23 taxa and 21 types), Myriapoda: 100 Individuals (21 taxa and 18 types); Nematoda: 2 Individuals (1 taxa); Plathelminthes: 11 Individuals (5 taxa); Protura: 4 Individuals (3 Taxa); Tardigrada: 2 Individuals (2 taxa); Diptera: 1 Individual. 2017-10-27

How to cite: Christian, A., Decker, P., Wurst, E. & W.E.R. Xylander: VIRMISCO — The Virtual Microscope Slide Collection. www.virmisco.org.

Publication: Decker, P., Christian, A. & W.E.R. Xylander (2018): VIRMISCO – The Virtual Microscope Slide Collection. – ZooKeys 741: 271-282.  Download PDF