Re: OME Compliant Specification

Posted by Jason Swedlow on
URL: http://confocal-microscopy-list.275.s1.nabble.com/OME-Compliant-Specification-tp5122114p5125001.html

Hi Michael-

Fully agreed; see response to Mark Cannell.

It's exactly why we do all the specification work AND develop,
maintain and release Bio-Formats (see
http://www.openmicroscopy.org/site/products/bio-formats for more
info).

Cheers,

Jason

On Tue, Jun 1, 2010 at 8:43 AM, Michael Weber <[hidden email]> wrote:

> JY,
>
> manufacturers might prefer a proprietary file format because
> (a) it binds the customer to proprietary software sold by the same company
> and (b) its development/future remains under control of the company.
> I am pretty sure that the majority of customers uses image processing
> software that comes with the microscope, or is at least distributed by the
> same manufacturer. And the latter might fear unforeseeable developments of
> the file format, such as a sudden death.
>
> Don't get me wrong, I like the idea of a standardized file format for
> microscopy, but I doubt that it will ever come - at least not as a direct
> output of a company's acquisition software. The situation is quite
> comparable to the photography market: every manufacturers has its own raw
> format, a group of customers screams for support of a standardized format
> such as png, but nothing really changes. A reasonable way (or
> work-around?) would be to have a converter which automatically turns the
> proprietary files into a single file format. In fact it does exist in form
> of Bio-Formats.
>
> Michael
>
>
>> On May 31, 2010, at 4:59 PM, Jason Swedlow wrote:
>>
>>> Dear All-
>>>
>>> Today, we are publishing a commentary on file formats in the Journal
>>> of Cell Biology.  The full text is available at:
>>>
>>
>> [snip.]
>>
>>>   New file formats should not be created
>>> with every new software release.  At the very least, the option of
>>> writing data to open, standardized file formats must be supported in
>>> all software, whether open or proprietary.  We understand that
>>> exceptional cases exist where specialized image data or metadata
>>> require proprietary, custom formats.
>>
>> Hi Jason.
>> Fantastic work; the paper is excellent.
>> But maybe we could turn the above fact upside down, and ask questions
>> to manufacturers:
>> - If you are a software engineer working for a microscope company, why
>> did you chose to create a new file format instead of using existing,
>> open ones?
>> - Is there missing features, e.g. in OME specification that made you
>> chose to go for your own?
>> - If they were implemented in OME 'tomorrow', will your product go for
>> OME format?
>>
>> I guess there is people working for Zeiss, Leica, Olympus, etc..
>> reading this mailing-list. Maybe they could care to give us a clue as
>> why?
>>
>> Best
>> jy
>>
>>
>>
>>
>> --
>> Jean-Yves Tinevez
>> PFID - Imagopole
>> Institut Pasteur
>> 25-28, rue du Docteur Roux
>> 75724 Paris cedex 15
>> France
>> tel: [phone]
>

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