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Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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Provide support for iiif images in Bioformats #3245

Closed imoutsatsos closed 5 years ago

imoutsatsos commented 6 years ago

The international image interoperability (iiif) framework is a widely adopted and open source supported image format. Multiple iiif compatible deep zoom image viewers and servers are developed by open source communities in the cultural heritage (read museums) and library domains. These tools are now finding increasing adoption in the biological imaging space. As a result, it would be useful if bioformats was to also support reading images and metadata from iiif servers. The iiif Image API is described here: https://iiif.io/api/image/2.1/

Thank you for your consideration and best regards Ioannis

manics commented 6 years ago

@imoutsatsos Thanks for pointing it out to us. We're currently doing some work on supporting remote resources in BioFormats. For example, the development branch of BioFormats has some support for reading directly from URLs https://github.com/ome/ome-common-java/blob/v5.3.7/src/main/java/loci/common/URLHandle.java and support for S3 object stores is in progress https://github.com/ome/ome-common-java/pull/33

If you're interested in contributing support for IIIF the above should help you get started.

ebremer commented 5 years ago

@imoutsatsos I have built a IIIF tiling server named ImageBox based on Bioformats. I will be releasing it to the public in a couple of months after some additional development and testing. It was very much developed with whole slide imaging in mind.

ebremer commented 5 years ago

ImageBox was first mentioned in this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333212/ Some of the links may be broken/out-of-date, but there will be updated links when ImageBox is released.

ebremer commented 5 years ago

Here's the working demo page that will be submitted with the ImageBox2 paper: http://imagebox.ebremer.com

ebremer commented 5 years ago

My paper was submitted and the code is now available. The code is alpha and some additional features need to be implemented for full IIIF compliance, but it works. The one unusual feature of ImageBox is that it can provide tiles over HTTP using HTTP range requests (as well as files local to the ImageBox2 instance). The demo server runs on a non-cloud server server and pulls tiles from a WSI SVS image located on the Amazon S3 cloud. It is fairly performant I believe. I will be doing additional work over the next march of months to make it fully robust, but appreciate any feedback and/or comments.

joshmoore commented 5 years ago

@ebremer. Going slightly beyond my ❤️ , I've been wondering what the next best step would be here, since this issue really isn't needed any more. What do you think about posting under https://forum.image.sc/c/announcements with the tags you think are appropriate, and let's see if we can't kick off some uptake?

All the best, ~Josh

sbesson commented 5 years ago

Seconding @joshmoore's suggestion to post your work on image.sc to further promote your work. Also looking forward to reading your paper about ImageBox2. Is it already available on biorxiv or similar preprint mechanism?

ebremer commented 5 years ago

@joshmoore @sbesson I would be happy to post something on https://forum.image.sc/c/announcements. Let me write up some more documentation for early adopters. It's not available on any pre-print mechanism yet but I will be happy to share the URL when it is available.