Science Goes Digital

January 18, 2016 ZEISS Microscopy

How digitization saves historical microscopy archives

Digitization is impacting every facet of our lives. Science is no different. Digitization is changing how we handle scientific knowledge. Generating and disseminating scientific knowledge is easier than ever. Digital storage and analytical instruments make it possible to quickly structure and analyze large, complex quantities of microscopy data and make them available to a broad audience.

Digitizing the Blechschmidt collection with ZEISS Axio Scan.Z1 and ZEN 2 slidescan
Digitizing the Blechschmidt collection with ZEISS Axio Scan.Z1 and ZEN 2 slidescan

Qualitative data collection has turned into quantitative data collection, making research results more reliable and more conclusive. Communication technologies are taking collaboration between research teams to a whole new level. Globally networked research projects are no longer the exception to the rule: they are now the norm. Digitization has changed the sciences from the ground up. ZEISS Microscopy was at the forefront of the evolution in digitization and has developed a system for virtual microscopy. ZEISS Axio Scan.Z1 digitizes quickly and, being a highly automated system, processes a large number of samples using a multitude of recording modalities, underscoring the broad application range of the system. Axio Scan.Z1  is now being used to digitize historical collections of embryological specimen slides with the goal of ultimately making them available to researchers and the general public.

 

Case in point: The Digital Embryology Consortium

Dr. Mark Hill in the new scanner room of the Blechschmidt Collection in Göttingen, Germany. The monitor shows the scan of a sagittal cross-section through a human embryo.
Dr. Mark Hill in the new scanner room of the Blechschmidt Collection in Göttingen, Germany. The monitor shows the scan of a sagittal cross-section through a human embryo.

The goal of the Digital Embryology Consortium (DEC) is to preserve and protect the large collections of specimen slides from human embryology, make them available to both researchers and the public online for free and thereby protect the valuable original specimens. Many of the historic collections are almost 100 years old. The members of the consortium are: the UNSW Australia, the University of Göttingen (Blechschmidt Collection), the Natural History Museum in Berlin (Hubrecht Collection), the Ruhr University Bochum (Hinrichsen Collection), Complutense University of Madrid (Madrid Collection), the University of British Columbia (Perry-Arey-Milligan Collection), the National Museum of Health and Medicine (Carnegie Collection) and Kyoto University (Kyoto Collection).

Dr. Mark Hill from the School of Medical Sciences at the UNSW Australia had the idea for this enormous project. Hill states that “over the years collection slides have been lost, misplaced, damaged or their histology stains degenerated never to be seen again. Scanning will preserve these collections as they now stand against future losses.” The project is funded by a grant to the UNSW Foundation. Hill has been in constant contact with different institutes and the curators of various museums to gain their support for this project. On 8 April 2015, the members of the consortium met in Göttingen to finally celebrate the start of this project. Key elements for the success of this project are the scanner and data management. After Hill had tested slide scanners from various manufacturers he ultimately chose ZEISS Axio Scan.Z1. Ease of use, the size of the microscope slides, the resolution, throughput, file format and transportability were all key factors in Hill’s decision.

 

Quality & Customization

Overview image of a typical 2"x 3" microscope slide with serial sections taken from the Blechschmidt Human Embryology Collection, Göttingen, Germany
Overview image of a typical 2″x 3″ microscope slide with serial sections taken from the Blechschmidt Human Embryology Collection, Göttingen, Germany

There were a lot things going for the ZEISS system. In addition to its resolution, the digital slide scanner scored big by making it possible to use different sizes of microscope slides. Historical slides are very often not compatible with every slide scanner on the market as they tend to feature different sizes and dimensions than the standardized glass slides used today. For example, ZEISS was able to offer custom mounting frames for the archive of the Kyoto Collection that accommodate the special shapes of the slides in this collection, demonstrating the strengths of ZEISS Axio Scan.Z1. Furthermore the slide scanner is also easy to transport and set up when moving from one collection to the next. Special transport boxes, normally intended for demo systems, are being used.

 

“Over the years collection slides have been lost, misplaced, damaged or their histology stains degenerated never to be seen again. Scanning will preserve these collections as they now stand against future losses.”

Recognizing the benefits of digitization

From the Blechschmidt Collection: Trigeminal ganglion (above) with the exiting maxillary nerve (below).
From the Blechschmidt Collection: Trigeminal ganglion (above) with the exiting maxillary nerve (below).

Four of the consortium members met with ZEISS specialists at the launch event at the University of Göttingen. Consortium member Prof. Chistoph Viebahn gave the opening address. Dr. Thorsten Heupel, Product Manager for ZEISS Axio Scan.Z1, had already given a detailed two-day introduction to the system. The Blechschmidt Collection in Göttingen is the starting point for the digitization project. The team already digitized more than 4,000 slides and created over 40 TB of data during the first round. Once they’re finished, the system will be transported to the other consortium members. The project is scheduled for completion by the end of 2017. The data will be available online through the free software OMERO which is compatible with the ZEISS CZI image format. The benefits of digitization are obvious. The virtual slides can be examined just as if you were using a real microscope but no special instrument or even the actual slide is required. This protects the original slides and at the same time makes them available for simultaneous viewing, analysis and study around the world; furthermore, digitization supports data mining, which will become more and more important in the future.

 

From the Blechschmidt Collection: Detailed view of the region of origin
From the Blechschmidt Collection: Detailed view of the region of origin of the maxillary nerve.

The German Research Foundation (DFG) already recognized how research will benefit from digitization, as stated in a press release from March 2014. The development of standards for the photographic documentation of permanent microscope slide mounts in precarious mounting media is just one of 12 projects at museums, universities and non-university institutes which the DFG is supporting with the aim of electronically indexing research collections, digitizing the objects and making them accessible online. The projects focus on different object categories, including herbaria, a historical skeletal collection, old book covers and a collection of historical musical instruments. The 12 projects with a total of 4.3 million euros in funding are of interest to a variety of research communities.

 

 

 

 

ZEISS Axio Scan.Z1 at the Natural History Museum, London
ZEISS Axio Scan.Z1 at the Natural History Museum, London

An open design supports new applications

Having seen the benefit of and necessity for this process, there is a growing interest to digitize every kind of specimen imaginable. For example, ZEISS Axio Scan.Z1 has already been installed in the Natural History Museum in London to support their endeavors. In addition to making collections accessible for performing basic research, virtual microscopy opens up new possibilities in telepathology, where the results from microscopes and the lab are digitally transferred to medical specialists for interpretation and diagnosis. Due to the open design and customization options in hardware and software, ZEISS Axio Scan.Z1 is also used in high throughput applications with geological slides or cryohistology of mineralized tissue.

 

 

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