[ome-users] JPEG XR compression support is coming to Bio-Formats

Jason Swedlow (Staff) j.r.swedlow at dundee.ac.uk
Wed Aug 31 12:43:40 BST 2016

Dear All-

Just to follow up on this— as you probably gleaned from Helen’s email, we’ve been pursuing several ways to fund the many aspects of our work so we can deliver the tools and resources the community needs. Some of these are in standard grants- more about recent progress in funding OME in an upcoming email. Some involve collaborations with industrial partners; others involve specific projects and applications (the BBSRC-funded IDR is an example of this).

Today’s entry in the OME blog (http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/) discusses examples of ways we are working with industrial partners to ensure that the range of tools and capabilities required by the community are delivered. The blog describes two examples of working with commercial imaging companies, namely 3i and ZEISS Microscopy, to deliver readers for Bio-Formats. File formats readers are particularly challenging to fund, for obvious reasons.  With 3i and ZEISS, we’ve come up with creative ways to deliver work the community needs. We hope these serve as examples and templates for further collaborations with the industrial imaging community. Our thanks to 3i and ZEISS for their open and forward-looking approach to delivering solutions for the community of imaging scientists.

We welcome feedback and ideas from the OME user and developer community on these issues.  Overall, we must diversify our funding sources.  More about the broader funding strategy in a future email.

As always, thanks for your support.



Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee

Phone:  +44 (0) 1382 385819
email: j.swedlow at dundee.ac.uk<https://dbxprd0410.outlook.com/owa/redir.aspx?C=XlY__cjOnUCLrUuc7zPnSr5hht0k884Icce5AfHAhv6fHZjWmwxAigQ84T9_MIRi02LghCy2-Tk.&URL=mailto%3aj.swedlow%40dundee.ac.uk>

Web: http://www.lifesci.dundee.ac.uk/people/jason-swedlow<https://dbxprd0410.outlook.com/owa/redir.aspx?C=XlY__cjOnUCLrUuc7zPnSr5hht0k884Icce5AfHAhv6fHZjWmwxAigQ84T9_MIRi02LghCy2-Tk.&URL=http%3a%2f%2fwww.lifesci.dundee.ac.uk%2fgre%2fstaff%2fjason-swedlow>
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From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk> on behalf of Helen Flynn (Staff) <h.flynn at dundee.ac.uk>
Sent: Tuesday, August 30, 2016 2:01:02 PM
To: ome-users at lists.openmicroscopy.org.uk; ome-devel at lists.openmicroscopy.org.uk
Subject: [ome-devel] JPEG XR compression support is coming to Bio-Formats

Dear All,

We are delighted to announce that thanks to a collaboration between Glencoe Software and Carl Zeiss Microscopy GmbH, support for whole slide images compressed with the JPEG XR compression scheme is coming to Bio-Formats.

Jason Swedlow says "We are particularly excited that the software we build in this collaboration will be available for anyone to download and use. This is a great example of how industrial partners can work together and build important capabilities that benefit the global scientific and pathology imaging communities. The work we do together will benefit users of ZEISS Axio Scan.Z1 and indeed anyone who uses JPEG XR compression in their image data."

This development will allow researchers, pathologists and imaging specialists working with these images worldwide to use a whole range of open source tools that rely on Bio-Formats for image file translation.


The OME Team

Dr Helen Flynn
OME Technical Writer
Centre for Gene Regulation & Expression
Open Microscopy Environment
University of Dundee

The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096
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