Slide Scanning

Mark Hill and Axio Scan.Z1

The Digital Embryology Consortium is using a Zeiss AxioScanZ1 scanner for the digitisation of collections. Slide scanning commenced in April 2015 at the Blechschmidt Collection, University of Göttingen, Germany.

Note that some collections, including the initial server test images, have come from pre-existing digital images from other scanners that are also included in the image database.

Oversized slides are also scanned and documented at a low resolution using a flatbed scanner, an CanoScan 9000F Mark II.

DEC OMERO Server

DEC Users (June 2017)
Mark Hill Christoph Viebahn Beate Brand-Saberi Peter Giere Shigehito Yamada	José Rodríguez-Vázquez Rosa Mirapeix Susan Lindsay Elizabeth Lockett Virginia Diewert	Maria Angeles de Miquel Wouter Lamers Bernadette de Bakker Joerg Maenner Hans-Georg Sydow	José Sanudo Joy Richman Janet Kerwin Yuzhu Cheng Steven Lisgo	Gregor Hagedorn Robert Anderson Nenad Maricic MCSU
Contact Mark Hill	DEC Image Server		DEC OMERO training manual (PDF)

Slide Scanner

Only users that have been trained in the Axio Scan.Z1 operation should operate the machine.


Zeiss Axio-Scan Z1	This plaque is attached to the scanner and acknowledges the contribution of the UNSW Foundation donor.

Scanner Transport

The Zeiss AxioScanZ1 scanner is transported to each embryo collection location using a purpose designed transport box. That allows simplified storage and transport of the scanner and all the required accessories. Note that the scanner requires Zeiss technical support for its initial set up at each location. My special thanks to Felton Global Logstics for their assistance with scanner shipping.


This photograph shows the Axio-Scan inside its transport case, with both case sides removed.	This photograph shows the Axio-Scan inside its transport case, with half of the case removed.

The space under the transport table is designed for storage of both accessories and the associated computer.


Accessory storage space	Computer storage space

Flatbed Scanner

Oversized slides are now also scanned and documented at a low resolution using a CanoScan 9000F Mark II. This is a high resolution CCD scanner, modern LIDE scanners have a very shallow depth of field not suitable for thicker glass slides.

The scanning protocol is transparency positive mode (unsharpen 9600 dpi). A lower resolution flatbed scan is also made to capture the slide label information, that is not visible in the transparency positive mode.

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