Re: OME Compliant Specification

Posted by Emmanuel Gustin on
URL: http://confocal-microscopy-list.275.s1.nabble.com/OME-Compliant-Specification-tp5122114p5125067.html

For a slightly more optimistic view, allow me to refer to flow cytometry:
The ISAC-defined FCS format (currently 3.0) is widely supported, AFAIK
by most instruments currently on the market. It has some gaps, for example
there is a lack of conventions for file naming and storing well coordinates
for the increasing number of instruments with autosamplers. Nevertheless,
if you read the file format specification carefully, it is possible to
write code that will read the output of instruments of a number of
different suppliers, and equally important, different generations of
instrument as well.

A good standardized format needs to be flexible and allow space for people
who need to store extra data in addition to those foreseen (as required or
optional) by the standard. I think a well-designed standard would actually
be welcome to most software developers at imaging companies, because defining
a really good file format is not easy. (In the past -- no reflection on
present company -- I've found quite a few nasty surprises in proprietary
file formats.) We should not hope to cover 100% with any standard format,
but 80% would already be a big step forward.

And in fairness, it should be pointed out that in recent years, the
manufacturers *have* become open to the idea: Today the problem is more
the inability of the user community to set up a strong representation and
agree on what they actually want. Or to find funding for the development
of a standard.

I think that is surprising, because the need of standard data formats in
biological imaging is quite high. All but the smallest laboratories and
teams have different types of instruments, optimal for specific application
ranges, and they need to be able to analyze, manage and review data in
a somewhat consistent manner. That forces many groups to adopt some kind
of internal "standard" anyway, and they can't always make good choices.

I suspect a factor here is that data standards tend to go hand in hand with
quantitative analysis, and so much imaging is still only qualitative.

My personal view is very strongly that I want the *primary* output of an
instrument, any instrument, to be in a open format that can at least
be read without great effort; it should be well-documented and well-designed.
The ability to convert data from a proprietary format to a secondary export
format is at best a stop-gap, *especially* for large volumes of data. (But
I particularly loathe "exports to Excel" that generate files without proper
headers and often no predictable structure.)


Best Regards,

Emmanuel


--
 Emmanuel Gustin,    Tel. [phone],    e-mail: [hidden email]


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michael Weber
Sent: dinsdag 1 juni 2010 09:44
To: [hidden email]
Subject: Re: OME Compliant Specification

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]