[ome-users] Bug report for version 2012-06 OME-XML in Fiji, seen in grid/collection stitching

[Roger Leigh]

On 10/11/16 14:34, Curtis Rueden wrote:
> Hi Roger,
>
>> I've done some further testing with the submitted files.
>
> Thank you very much for the further testing.
>
>> Workarounds for broken data should never compromise the handling of
>> valid data, and at some point there is a limit for what it is
>> reasonable or safe for us to correct.
>
> I absolutely agree 100%. However, two points in this case:
>
> 1) I believe these files were written by Bio-Formats itself. I would
> argue that under no circumstances should Bio-Formats write OME-TIFFs
> which are later considered to be invalid or corrupt. Even dev builds of
> Bio-Formats should use a stable schema version by default. If it is
> needed for testing to write files with "in-progress" schemas, that
> option should be specified via a manually triggered API call, rather
> than happen by default.
>
> 2) For files with an "in-progress" schema version, making a best effort
> to parse using nearby stable schema versions does not introduce any
> possibility of compromise to valid data handling. So I am glad to hear
> that Bio-Formats does this.

Hi Curtis,

Thanks for those suggestions.

For future Bio-Formats releases, the OME data model will be developed
and released mostly independently of Bio-Formats, which is now in a
separate github repository, built with maven.
https://github.com/ome/ome-model/


Regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

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