Whole slide imaging - hosting images online for sharing between institutions, how do you do it?

[Cromey, Douglas W - (dcromey)-2]

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One of the beauties of scanned microscope slides is the possibility of sharing data between colleagues without having to ship a box of fragile (and valuable) microscope slides between institutions. That said, scanned microscope slides are often pretty large data files and running a file server is often a job best left to IT pros.

If your institution has a semi-user friendly way of sharing this kind of data online, how do you do it? Do you outsource the hosting or do you have an internal mechanism? Do you have a mechanism for dealing with data that is also HIPPA compliant? Our institution's BOX license does not allow files larger that 15GB, which makes that not a useful option.

Thanks!
Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Associate Scientific Investigator
Dept. of Cellular & Molecular Medicine, University of Arizona
Life Sciences North, Room 463
1333 N. Martin Ave, Tucson, AZ  85721 USA

office:  LSN 463        email: [hidden email]<mailto:[hidden email]>
voice:  520-626-2824       fax:  [phone]

UA Microscopy Alliance - http://microscopy.arizona.edu/
A collaborative effort to bring information about shared microscopy
facilities to the University of Arizona and the community.

[Sathya Srinivasan]

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Dear Doug,
We have a few slide scanners generating huge amounts of data where we have
to set up naming of the files (as discussed previously in this list) and
storage, sharing and retrieval of the data based on the users like
Clinical, Research and Educational. One of the major issues which will show
up is if you have to deal with hospital samples and patient data
identifiers. We have to set up labeling to make sure it is secure and have
servers which are encrypted and password protected to provide access to
different areas of the server to different types of users. What we
understand from our experience is that there is no one solution. We use
data management software and use barcode labels on our slides. The labeling
starts from tissue collection, embedding, sectioning, staining, microscopy
imaging, storage, image analysis and data retrieval and sharing - and all
other things inbetween. I started collecting info about the advantages and
disadvantages of various methods. A mix and match workflow based on the
available resources is the best way to go. Still we see some of the data
management software does not talk with the imaging readers or image
analysis software as they come from different vendors besides the local IT
security/ encryption issues. Also, one has to make sure that those who
access those images have the right software on their system to open,
annotate, etc.

The following articles helped me during my "Task Force" meetings and gave
us some direction while setting up our model:

- Name It! Store It! Protect It!: A Systems Approach to Managing Data in
Research Core Facilities (
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5667402/) - which deals with
labeling conventions, data storage and other useful tips.

- Managing and Querying Whole Slide Images (
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3405921/)

-  A Practical Guide to Whole Slide Imaging: A White Paper from the Digital
Pathology Association (https://pubmed.ncbi.nlm.nih.gov/30307746/)

- A call for public archives for biological image data (
https://pubmed.ncbi.nlm.nih.gov/30377375/)

- BioHPC Cloud from UT Southwestern Medical Center (
https://portal.biohpc.swmed.edu/content/about/systems/) - has some detailed
plans and can adopt a few ideas from them. There are many fantastic data
storage/ retrieval setups from other institutions too.

The above is just the tip of the iceberg! Good luck!

Sathya Srinivasan
Imaging and Morphology Support Core
ONPRC
Beaverton, OR 97006



On Mon, Feb 8, 2021 at 7:30 AM Cromey, Douglas W - (dcromey) <
[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> One of the beauties of scanned microscope slides is the possibility of
> sharing data between colleagues without having to ship a box of fragile
> (and valuable) microscope slides between institutions. That said, scanned
> microscope slides are often pretty large data files and running a file
> server is often a job best left to IT pros.
>
> If your institution has a semi-user friendly way of sharing this kind of
> data online, how do you do it? Do you outsource the hosting or do you have
> an internal mechanism? Do you have a mechanism for dealing with data that
> is also HIPPA compliant? Our institution's BOX license does not allow files
> larger that 15GB, which makes that not a useful option.
>
> Thanks!
> Doug
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Douglas W. Cromey, M.S. - Associate Scientific Investigator
> Dept. of Cellular & Molecular Medicine, University of Arizona
> Life Sciences North, Room 463
> 1333 N. Martin Ave, Tucson, AZ  85721 USA
>
> office:  LSN 463        email: [hidden email]<mailto:
> [hidden email]>
> voice:  520-626-2824       fax:  [phone]
>
> UA Microscopy Alliance - http://microscopy.arizona.edu/
> A collaborative effort to bring information about shared microscopy
> facilities to the University of Arizona and the community.
>