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.