Open Microscopy Environment

Posted: **Tue Dec 13, 2016 11:30 am**

Hi,

I'm in the process of writing an application which converts from a proprietary dataformat to OME-TIFF using the C++ libraries (ome-files-cpp 0.2.2, ome-common 5.3.2, bioformats 5.2.3).

I want to write multiple 2D images/datasets as series into one OME TIFF file.
This works, but I'm struggling to add specific metadata for each series

Code: Select all: for(auto dsn : matches) { // read each image dimensions from the dataset ReadImageDimensions(dsn, dims); // create meta data as we now know the image size shared_ptr<ome::files::CoreMetadata> meta = CreateMetaDataForImage(dims[0], dims[1]); meta->seriesMetadata.set("HDF5 Source Dataset", "some string"); metadataStore->setImageID(ome::files::createID("Image", idx), idx); fillPixels(*metadataStore, *meta, idx); ome::xml::meta::OMEXMLMetadata& omexml(dynamic_cast<ome::xml::meta::OMEXMLMetadata&>(*metadataStore)); ome::files::addMetadataOnly(omexml, idx); idx++; }

I've now looked at the generated TIFF file using

Code: Select all: ome-files info --omexml

Image: file_with_one_raw_image_raw_img.ome.tiff
Using reader: OME-TIFF (Open Microscopy Environment TIFF)
Reader setup took 00:00:00.083000

Filename = "/.../file_with_one_raw_image_raw_img.ome.tiff"
Used files = ["/.../file_with_one_raw_image_raw_img.ome.tiff"]

Reading core metadata
Series count = 1

Series #0:
Image count = 1
RGB = [false] ([1])
Interleaved = false
Indexed = false
Width = 3000
Height = 2000
SizeZ = 1 (effectively 1)
SizeT = 1 (effectively 1)
SizeC = 1 (effectively 1)
Thumbnail size = 128 × 85
Endianness = little
DimensionOrder = XYZTC (certain)
PixelType = uint16
Bits per Pixel = 16
MetadataComplete = true
ThumbnailSeries = false

Global metadata:
HDF5 File Version: 0.1
HDF5 Source File: /.../file_with_one_raw_image.h5
HDF5 Storage Server compilation timestamp: Jan 29 2016 17:50:06
UserComment: someComment

OME-XML metadata:
<?xml version="1.0" encoding="UTF-8" standalone="no" ?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" UUID="urn:uuid:2cb9eadf-7f62-42f6-a81d-cd9095590a7a" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/O ... 06/ome.xsd"><Image ID="Image:0"><Pixels BigEndian="false" DimensionOrder="XYZTC" ID="Pixels:0" Interleaved="false" SignificantBits="16" SizeC="1" SizeT="1" SizeX="3000" SizeY="2000" SizeZ="1" Type="uint16"><Channel Color="-1" ID="Channel:0:0" SamplesPerPixel="1"/><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="file_with_one_raw_image_raw_img.ome.tiff">urn:uuid:2cb9eadf-7f62-42f6-a81d-cd9095590a7a</UUID></TiffData><Plane TheC="0" TheT="0" TheZ="0"/></Pixels></Image><StructuredAnnotations><XMLAnnotation ID="Annotation:0"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 File Version</Key><Value xmlns="">0.1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:1"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 Source File</Key><Value xmlns="">/.../file_with_one_raw_image.h5</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:2"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 Storage Server compilation timestamp</Key><Value xmlns="">Jan 29 2016 17:50:06</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:3"><Value><OriginalMetadata xmlns=""><Key xmlns="">UserComment</Key><Value xmlns="">someComment</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:4"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 File Version</Key><Value xmlns="">0.1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:5"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 Source File</Key><Value xmlns="">/.../file_with_one_raw_image.h5</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:6"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 Storage Server compilation timestamp</Key><Value xmlns="">Jan 29 2016 17:50:06</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:7"><Value><OriginalMetadata xmlns=""><Key xmlns="">UserComment</Key><Value xmlns="">someComment</Value></OriginalMetadata></Value></XMLAnnotation></StructuredAnnotations></OME>
OME-XML validation successful

but my metadata series entry seems to be not there.

Any hints what I'm doing wrong?

Posted: **Wed Dec 14, 2016 11:53 am**

The "Series Metadata" in CoreMetadata is filled when reading an image; this is typically reader-specific key-value pairs for format-specific metadata which isn't represented by the OME-XML data model, and is for the most part completely independent of the OME-XML metadata other than setting them from OriginalMetadata annotations where present. It's not (currently) used when writing; the series metadata is not used at all.

This is certainly something we can change; we could make the MetadataTools fill functions create OriginalMetadata annotations from these core metadata objects.

I created https://trello.com/c/mJfifiAq/54-save-s ... adatastore to track this.

For now, I would suggest looking at creating a custom XML Annotation using e.g. OriginalMetadataAnnotation Java or C++). An example of how to use it is here; a similar thing could be done with OME Files C++. However, we're unhappy with the usability of this, and are currently investigating a much more general and user-friendly way of working with custom annotations, which we hope to have in place for the upcoming OME Files C++ 0.3.0 release. This should make using the model much more transparent.

Kind regards,
Roger

Posted: **Mon Feb 06, 2017 6:09 pm**

Thanks Roger. I went down the route you suggested.

Open Microscopy Environment

[C++] Adding metadata for series

[C++] Adding metadata for series

Re: [C++] Adding metadata for series

Re: [C++] Adding metadata for series