[ome-users] incell 2200 and 6000 bioformats support

[Roger Leigh]

On 12/12/16 09:41, Daniel White wrote:
> Hi Melissa and all,
>
> I have some dummy datasets from GE InCell 2200 and 6000
>
> 2200 is the successor of 2000, and has the same iimage and meta data
> formats.
> InCell 6000 also has the same formats.
>
> In the list of supported formats, it only say there is support for
> incell 1000, 2000 and 3000.
> But In Cell 2200 data seems to work pretty well.
>
> Could we add 2200 (and 6000) to the list of supported formats?
>
> How can I help accomplish that? (I work for GE)

Dear Daniel,

The first step would be for us to have some sample data which we can add
to our set used for daily integration testing.  If that was under a
permissive licence such as CC-BY
(https://creativecommons.org/licenses/by/4.0/) this would allow use of
them for wider testing and as public samples for the format (example of
ND2 datasets we make public:
http://downloads.openmicroscopy.org/images/ND2/).  If your dummy
datasets were under such a licence and you could make them available for
download, we would be happy to add them to our test datasets.  If you
wish to upload files to us directly,
http://qa.openmicroscopy.org.uk/qa/upload/ will allow the upload of a
zip file containing a dataset of up to 2GiB; if your data is larger we
can provide credentials to upload directly.

With the test data in place, we can run our testsuite and determine if
any code changes are needed.  It might be the case that no changes are
needed other than updating the documentation for 2200; 6000 is a bit of
an unknown until we know more details about it.

Is there a written specification available for the formats?

Regarding work needed to support the formats, should any changes be
required, being an open source project there are several options for
getting changes made, which include:

- us (OME) opening a ticket and doing the work as time and release
schedules permit
- GE making the desired changes to the InCell readers and opening a pull
request for review
- having a third party such as Glencoe Software (glencoesoftware.com) to
make the changes on a contract basis and then submit them to us via a
pull request


Kind regards,
Roger Leigh

--
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