[ome-users] Leica LOF data format

[Sebastien Besson (Staff)]

Hi Bryan and Michael,

Thanks for enquiring about the status of this. We certainly have a growing backlog of many tens of new file formats. Amongst these, the Leica LOF file format is definitely a highly requested one and we definitely received a private specification as indicated on the Leica LIF format page (https://docs.openmicroscopy.org/bio-formats/5.7.1/formats/leica-lif.html).

Developing and testing new file format readers is significantly more costly than maintaining existing ones. Besides the work on the new reader, there is the establishment of all the testing infrastructure (https://ci.openmicroscopy.org/view/Bio-Formats/). Our priorities are necessarily our current academic deliverables (http://www.bbsrc.ac.uk/documents/2016-trdf-bioimaging-awarded-grants/; https://wellcome.ac.uk/what-we-do/directories/biomedical-resource-technology-development-grants-people-funded), which do fund cross-platform resources for writing OME-TIFF (https://www.openmicroscopy.org/ome-files/) and support for several binary formats (BDV, etc.).  While we certainly want to support as many formats as possible, the seemingly eternal development of new formats is hard to prioritise, given other pressing needs.

On the other hand, we will review any external contribution with new reader additions and consider their inclusion in a minor release of Bio-Formats. Since the beginning of 2016, we have had several additions of this kind: PerkinElmer Columbus was developed for the IDR project, Olympus OIR and Zeiss CZI/JPEG-XR were funded by a partnership between Glencoe Software and the commercial developer of the formats and 3i Slidebook was developed and is maintained by the 3i team (http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/). Of course, we always welcome independent community contributions to Bio-Formats as well (https://www.openmicroscopy.org/contributors/).

We are dedicated to maintaining Bio-Formats, but also, in the best spirit of open source development, sourcing contributions from the community for new formats.  The alternatives listed above provide several avenues for adding LOF support to Bio-Formats.

Best,
The OME Team

On 5 Oct 2017, at 14:20, Cammer, Michael <Michael.Cammer at med.nyu.edu<mailto:Michael.Cammer at med.nyu.edu>> wrote:

Interesting.  Is this a problem at the BioFormats end or at the Leica end?

Michael Cammer, Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016
C: 914-309-3270  Michael.Cammer at med.nyu.edu<mailto:Michael.Cammer at med.nyu.edu>    http://microscopynotes.com/
https://med.nyu.edu/research/research-resources/scientific-cores-shared-resources/microscopy-laboratory


From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Bryan Crawford
Sent: Thursday, October 05, 2017 9:14 AM
To: ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: [ome-users] Leica LOF data format

Greetings,

I would like to add my voice to those of the many Leica SP8 users I’m sure you’ve heard from who are desperately hoping BioFormats will soon support the Leica .LOF data format.  We use Fiji every day.  We have just upgraded from an antique SP2 to a lovely new SP8, only to discover that we can’t open the files generated using Fiji because BioFormats doesn’t support this format.  From my searching on line, it appears that BioFormats received a specification document for the .LOF format from Leica last year (https://docs.openmicroscopy.org/bio-formats/5.3.4/formats/leica-lif.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.openmicroscopy.org_bio-2Dformats_5.3.4_formats_leica-2Dlif.html&d=DQMGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=83B3kTEKmZjrE9dXtxLGrPtsWYebJdr4dtgiP5jvkJQ&s=wu4xD5UlwxiyekSLB2OiHsFpkZQ5NUxVlq5Nl_Lghcw&e=>), but has not yet managed to include this format in the library.

My impression is that there are a significant number of SP8 systems installed world wide, so I would hope this is a high priority.  Can anyone provide more information about this?

Thank you.

P.S.  Please reply directly to bryanc at unb.ca<mailto:bryanc at unb.ca>, as I’m not a regular subscriber to this list

--
Dr. B.D.Crawford
Professor
Matrix Dynamics Lab
Department of Biology
University of New Brunswick
Fredericton, NB, Canada


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