[ome-devel] 3D data

[Eilidh Troup]

Hi Mark,

Thanks very much for this detailed response.

Eilidh

> On 14 Mar 2018, at 12:33, Mark Carroll <m.t.b.carroll at dundee.ac.uk> wrote:
> 
> On 03/12/2018 10:11 AM, Eilidh Troup wrote:
> 
>> I have a question from a potential OMERO user about 3D image data. How well would OMERO handle the following data?
>> 
>> We have large imaging datasets from our 3D plant phenotyping system. Not microscopy images but whole plants (growth over time). Would these fit with the OMERO database remit?  Our data format is .bmp files, a specialised analysis file for the 3D data (.npz), and .properties file.
> 
> There are various ways of combining 2D BMPs into time series that can
> then be scrolled through in OMERO.web and laid out in OMERO.figure. For
> example, there is the Combine Images script mentioned at
> http://help.openmicroscopy.org/scripts.html#utility and even at import
> time pattern files can be used as on
> https://docs.openmicroscopy.org/latest/bio-formats5.8/formats/pattern-file.html.
> 
> I would expect OMERO.tables at
> https://docs.openmicroscopy.org/latest/omero5.4/developers/Tables.html
> to fit nicely with the npz files and the properties files could become
> map annotations as at
> https://docs.openmicroscopy.org/latest/omero5.4/developers/Model/KeyValuePairs.html.
> However, one would need to write a simple script, perhaps using OMERO's
> API and/or gateways, to perform those conversions. Of course, arbitrary
> files may be directly attached to imaging data in OMERO.
> 
> In short: OMERO could probably handle the data well but to make it
> usefully viewable and queryable it would probably help to at least write
> a bit of Python code to slightly reprocess the data into something more
> OMERO-friendly, whether before or after import. OMERO offers a few
> options for exactly how that happens: for example, some of the
> properties file data may most appropriately be represented as tags in
> OMERO if some keys take few possible values.
> 
> I can't resist speculating that for your application regions of interest
> could be valuable too, perhaps via our MATLAB or ImageJ integration: for
> storing quantitative measurements from each image about how the plants
> are growing, then for subsequent querying and analysis over the time
> series. If the numpy arrays do include points or shapes then it could be
> worth writing a script to process, say, some of that npz data into OMERO
> ROIs.
> 
> If your data format is or may become widely adopted then it could be a
> good investment for you to write a Bio-Formats reader that turns the
> data into map annotations and ROIs at import time but I am guessing that
> some ad hoc client scripts are your best path forward for now.
> 
> Cheers,
> 
> Mark
> 
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