Open Microscopy Environment

Hello,

I have some problems retrieving metadata from a flex-file:

1)
I saw, that there are methods to get information about the objectives (NA, magnification...). In their function signature ther is a 'objectiveIndex' parameter to access the objectives attributes. However I couldn't find any way to determine the index from an attribute of the image plane that I'm currently reading.
This is the method from the 'metaDataRetrieve' class I would like to use to:
getObjectiveLensNA(int instrumentIndex, int objectiveIndex)
But where do I get the link between image and Objective from????

2)
Some methods of 'metaDataRetrieve' also need a 'pixelsIndex' parmeter. What does that refer to?


Here is the an extract of a matlab-script to get an idea how I use the API:
reader = loci.formats.in.FlexReader();
metaDataScheme = loci.formats.ome.OMEXML200809Metadata();
imageReader = loci.formats.gui.BufferedImageReader(reader);
imageReader.setMetadataStore(metaDataScheme)
imageReader.setId(absoluteFlexFilePath);
metaData = imageReader.getMetadataStore();

% Read the image planes.
for s = 1:imageReader.getSeriesCount();
imageReader.setSeries(s - 1);

for i = 1:imageReader.getImageCount();
img = imageReader.openImage(i - 1);
pix = img.getData.getPixels(0, ...
0, ...
imageReader.getSizeX(), ...
imageReader.getSizeY(), ...
[]);

zct = imageReader.getZCTCoords(i - 1);
imageIndex = imageReader.getIndex(zct(1), zct(2), zct(3));
attribute = metaData.getPixelsCount(imageIndex)
%etc.
end
end

Hi Felix,

I saw, that there are methods to get information about the objectives (NA, magnification...). In their function signature ther is a 'objectiveIndex' parameter to access the objectives attributes. However I couldn't find any way to determine the index from an attribute of the image plane that I'm currently reading.

There is currently no way to directly retrieve the Objective index from an Image index. What you need to do instead is the following:

Code: Select all

% retrieve the ID of the Objective linked to the given Image
objectiveID = metaDataScheme.getObjectiveSettingsObjective(imageIndex)
% check each Objective's ID to determine the index of the above Objective ID
numberOfObjectives = metaDataScheme.getObjectiveCount(0)
objectiveIndex = -1
for i = 0 : numberOfObjectives - 1
  if objectiveID == metaDataScheme.getObjectiveID(0, i)
    objectiveIndex = i
  end
end


Some methods of 'metaDataRetrieve' also need a 'pixelsIndex' parmeter. What does that refer to?

The 'pixelsIndex' is somewhat related to the 'imageIndex'. In OME-XML terminology, an 'Image' represents one or more stacks of 5D data that share properties (e.g. acquisition date). Each of the 5D stacks contained in an Image is a 'Pixels', so 'pixelsIndex' simply indicates which of the Pixels you want to access. Unless you are working with certain OME-XML and OME-TIFF files, 'pixelsIndex' should always be 0.

Note that OME-XML terminology is slightly different from Bio-Formats' terminology, in which an image refers to a single plane and a series refers to a single stack of 5D data. So in your code, 'imageIndex' should be equivalent to 's'.

Finally, MetadataRetrieve is based on the OME-XML schema; if you haven't already, I would strongly recommend that you read through the OME-XML schema (available at http://www.ome-xml.org), as it provides a better explanation of the metadata structure than is in the MetadataRetrieve documentation.

Regards,
-Melissa

Thanks a lot for your efficient and quick help.
Best regards,
Felix