Abstract
Digitisation allows scientists rapid access to research objects. For transparent to semi-transparent three-dimensional microscopic objects, such as microinvertebrates or small body parts of organisms, available databases are scarce. Most mounting media used for permanent microscope slides deteriorate after some years or decades, eventually leading to total damage and loss of the object. However, restoration is labour-intensive, and often the composition of the mounting media is not known. A digital preservation of important material, especially types, is important and an urgent need. The Virtual Microscope Slide Collection – VIRMISCO project has developed recommendations for taking microscopic image stacks of three-dimensional objects, depositing and presenting such series of digital image files or z-stacks as an online platform. The core of VIRMISCO is an online viewer, which enables the user to virtually focus through an object online as if using a real microscope. Additionally, VIRMISCO offers features such as search, rotating, zooming, measuring, changing brightness or contrast, taking snapshots, leaving feedback as well as downloading complete z-stacks as jpeg files or video file. The open source system can be installed by any institution and can be linked to common database or images can be sent to the Senckenberg Museum of Natural History Görlitz. The benefits of VIRMISCO are the preservation of important or fragile material, to avoid loan, to act as a digital archive for image files and to allow determination by experts from the distance, as well as providing reference libraries for taxonomic research or education and providing image series as online supplementary material for publications or digital vouchers of specimens of molecular investigations are relevant applications for VIRMISCO.
Highlights
Recent advantages in digitisation facilitate use, processing, duplication, distribution, archiving, and playback on common media devices, and improved applications for inquiries and comparison
While projects on virtual microscopy in biology or micropalaeontology are rare, in medical applications virtual microscopy and virtual slide collections are well known and acknowledged as beneficial e.g., for documentation, teaching, diagnoses, and research (Kumar et al 2004, Gu and Ogilvie 2005, Helin et al 2005, Krippendorf and Lough 2005, Goldberg and Dintzis 2007, Mikula et al 2007, Dee 2009, Weinstein et al 2009). These are mostly restricted to two-dimensional histological slices or cell biology, are not open source, are not accessible publicly online, restricted to a specific manufacturer or do not comply with the needs of a soil zoological collection
In this publication we introduce the open source system “the Virtual Microscope Slide Collection – VIRMISCO” to present digital microscope images of different focal planes
Summary
Recent advantages in digitisation facilitate use, processing, duplication, distribution, archiving, and playback on common media devices, and improved applications for inquiries and comparison. General recommendations for digitisation of three-dimensional collection objects on permanent microscope slides of soil fauna and other small organisms are provided.
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