[ome-users] How to get information from image

[Qi Gong]

Hello David,

Thank you for your email. I will play with those functions.

Regards,
Qi

On Tue, Dec 5, 2017 at 7:20 AM, David Gault (Staff) <d.gault at dundee.ac.uk>
wrote:

> Hi Qi,
>
> In the Bio-Formats developer documentation we have a section on handling
> whole slide images which may be of interest to you:Working with whole
> slide images
> <https://docs.openmicroscopy.org/bio-formats/5.7.2/developers/wsi.html>
> There is also a short example on reading sub resolutions: https://github.
> com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/utils/
> SubResolutionExample.java
>
> More generally, in Bio-Formats access to metadata is provided via the
> MetadataStore and MetadataRetrieve interfaces. In this instance we would
> use MetadataRetrieve to access getters for all of the available metadata in
> the OME-XML model objects.
> MetadataRetrieve can be used as below and a full list of the available
> getters can be found at https://downloads.openmicroscopy.org/bio-
> formats/5.7.2/api/loci/formats/meta/MetadataRetrieve.html
>
> ServiceFactory factory = new ServiceFactory();
> OMEXMLService service = factory.getInstance(OMEXMLService.class);
> MetadataRetrieve retrieve = service.asRetrieve(reader.getMetadataStore());
>
>
> Additionally Bio-Formats also stores original metadata which is not a part
> of the OME-XML model as key value pairs. The metadata stored here will
> differ depending on the specific format being read. These values can be
> accessed using the FormatReader interface as shown below:
>
> // to retrieve original metadata specific to the current seriesHashtable<String, Object> seriesMetadata = reader.getSeriesMetadata();
>
> // to retrieve original metadata not unique to the series
> Hashtable<String, Object> globalMetadata = reader.getGlobalMetadata();
>
>
> I hope that is of help as a starting point but if there is still specific
> metadata fields which you are still unsure how to access please do let us
> know along with the format you are using and we can help further.
>
> With Thanks,
> David Gault
>
> On 4 Dec 2017, at 21:36, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>
> Hello everyone,
>
> We use Bioformats to load whole slide imaging. Does anyone know what
> function we can use to get all WSI information (e.g. each level image size,
> apparent  magnification, MMP, Image Type, Image Depth, Compression Type,
> Compression Ratio, Organization...). Thank you.
>
> Regards,
> Qi
>
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