DEC January 2018 Newsletter
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Welcome to the January 2018 DEC newsletter, I try to keep these newsletters brief, more regular updates can be found on the DEC website. If you require additional information please contact me by email.
Collections Scanning Progress
We have now completed the second collection (Hinrichsen Collection) scanning and the Axioskan has been relocated to Museum für Naturkunde, Berlin scanning the Embryological Collection. I would congratulate Dr Peter Giere who was able to secure additional funding to support the staff required for the slide scanning process. I also thank Zeiss for technical support at the scanner installation and required software updates.
Scanning of the is part of Embryo Collections::Embryological Collection will be completed in 2018, and I am currently beginning to update the selection process and logistics of transporting the scanner to the next DEC member collection.
Oversized slides are now also scanned and documented at a lower 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 historic thicker glass slides. This flatbed scanner will also be shipped with the Axio Scan.Z1 to each collection location.
OMERO Server (version 5.4)
The new DEC Omero Image Server (5.4) http://18.104.22.168:8080 has now been stably running since installed in December 2017. Sample test images from the Blechschmidt and Hinrichsen collections have now also been successfully uploaded in the JPGXR format.
There are many test images uploaded to the DEC image server that users should be able to access. Please note that these are only test images and are not in the final DEC database structure/format. The Blechschmidt and Hinrichsen test images can also be accessed from the DEC website external links.
Several collections have also begun uploading test images in other formats to see if OMERO database generates the appropriate image pyramids. Please convert a few sample scanned histology images from your collection into the JPGXR format and then upload using the OMERO client software OMERO.insight. Once you have successfully completed the upload could you contact me by email. Please note the test images can be from any original histology scan or photograph that you may have as long as the JPGXR format is used for the upload. You will need to used the personal user name and password that I have previously sent by email.
I visited in December Prof. Ralf Radlanski at the Charité - Campus Benjamin Franklin at Freie Universität Berlin. It gives me great pleasure to now announce the is part of Embryo Collections::Radlanski Collection as part of the DEC. The Radlanski Collection consists of 22 human embryos and fetuses ranging from 18 to 270 mm CRL.
I remind all members that I am happy to contact any institution that holds an human embryological collection of known provenance to contribute to the DEC.
DEC Berlin Meeting December 2017
Following the scanner relocation an international opening meeting was held in Berlin (Monday 11 December, Final Program PDF). It was well attended by DEC member representatives and was an ideal opportunity to discuss progress, technical issues, the online database, and research applications based on the scanned slides. I would hope that we will be able to hold similar opening meetings in the future at the new scanner locations.
I was able to demonstrate the slide scanner and Dr Peter Giere provided a tour of both the Museum and the Embryological collection. This was also an opportunity to collect the final HDDs from Hinrichsen Collection scanning.
With best wishes for the new year!