DEC June 2017 Newsletter
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Collections Scanning Progress
We have now completed the initial collection (Blechschmidt) scanning and the Axioskan has been relocated to Bochum University scanning the Hinrichsen Collection. There are 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 test images can also be accessed from the DEC website external links. Note that also available from the initial 2015 setup date are a number of UNSW test images from a stage 22 embryo (10 micron transverse sections) using a different scanner.
Scanning of the Hinrichsen Collection will be completed in 2017, and I am currently beginning to update the selection process and logistics of transporting the scanner to the next DEC member collection.
OMERO Server (version 5.3)
The new DEC Omero Image Server (5.3) http://126.96.36.199:8080 has now been stably running since installed in April 2017. Sample test images from the Blechschmidt collection have now also been successfully uploaded in the JPGXR format. Note that the new server has a different web address extension (8080) from the original server (4080), if you have added bookmarks to the earlier address they will no longer function. The server software will be updated to the latest version (5.3.2) after testing remote access options.
DEC OMERO Training Manual
I have included below links to a training manual specifically designed to help users with this process using OMERO.insight. This is manual is a 27 Mb PDFand therefore too large to attach to this current email. The manual is an edited version of that publicly available directly from OMERO developers. OMERO.insight is the client software required to locally upload individual and batch images to the DEC server.
- Web Page Link: https://human-embryology.org/wiki/DEC_OMERO_Server#OMERO_Training_Manual
- Direct Link: https://human-embryology.org/images/2/2e/DEC-OMERO-training-manual-2017.pdf
Remote image upload testing by users
I would now like individual consortium members to test the remote uploading of JPGXR format images to the server from their collection. These test images can be at any resolution you may have available, but I would appreciate all details of the scanned image to be sent to me so that I can add information and links to the DEC website. Note that all users also have editing access to the DEC website and the image information can be also be added directly by users to the individual collections pages.
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.
Many thanks in advance for your assistance in this testing process, I am hoping that any issues that arise can then be discussed with the software developers. This type of external testing is essential to establishing a stable platform for all users to access and upload images in the future.
Advertising the DEC
Some users may have wondered why we have not more widely advertised the DEC or not yet published information within a scientific journal?
We had to initially relocate (2015) the DEC nameserver to an academic institution and carry out long-term server stability testing (2016). Until a recent update (April 2017) the OMERO database software did not support the DEC image format. I wish to acknowledge Zeiss support to the OMERO developers in making this now possible.
I also feel that the image database needs to have a significant number of images available online to interest researchers when they originally access the DEC.
Finally, I have seen many unsuccessful online scientific databases fail due to a combination of software bugs, instability, poor user interface, and a lack of sufficient testing. I am sure you will appreciate that we should resolve any such issues on our database before advertising to the wider researcher audience.
I am still happy for you to let colleagues know about the DEC and apply for user accounts. If required, I can also provide additional DEC information to local users or your institute.
DEC update meeting
- April 2016 at the 2016 NSW Australia and New Zealand Society for Cell and Developmental Biology (ANZSCDB) meeting a DEC information poster presentation (JPG version 320 KB or PDF version 66.5 MB) was given.
- June 2017 a meeting at the Georg-August-Universität Göttingen will provide an update on the DEC project, members are most welcome to attend, please contact the local organisers for more information.
I will also be visiting all the German DEC collections for an update in June/July 2017.