[ome-users] Loading a subset of a stack

[Thomas Julou]

Dear Roger,

Thank you very much for your answer and help.

>> 2. or to create a reader and then load the plane I want only.
>> but the metadata of all frames are still loaded during the reader creation?
>> 
>>> IFormatReader reader = new ImageReader();
> 
> Try adding here:
> 
> MetadataOptions options = reader.getMetadataOptions();
> options.setMetadataLevel(MetadataLevel.MINIMUM);
> 
>>> reader.setId(id);
>>> //seriesCount = reader.getSeriesCount();
>>> sizeZ = reader.getSizeZ();
>>> sizeC = reader.getSizeC();
>>> sizeT = reader.getSizeT();
>>> imageCount = reader.getImageCount();
>>> IJ.log(sizeT + " frames.");

This looks like exactly what I was after. Unfortunately, when I tried it with a 5gb dataset produced by micromanager (supposably ome.tif stacks), I don’t get any significant change in performance. I guess it is due to how this specific reader is implemented :(

> The default behaviour is to read all metadata.  The above two lines
> should set it to read a minimum amount of metadata.  However, please
> note that this is dependent upon the implementation details of the
> individual readers and file formats; you may or many not see any
> difference in speed.  It will also mean if you need the extra metadata
> you'll need to reopen the image since it's parsed once when you
> initialise the reader.

Thanks for the detailed explanation.

> I should also point out that recent work has been done to improve the
> performance of Bio-Formats with files on network storage which should be
> in the upcoming 5.1 release.  You may find that this will provide
> significant improvements, though it will depend upon the file
> format/reader in question.

As mentionned above, I’m mostly using micro-manager dataset. Do you know whether any work has been done on this?
Or can you explain me where to find the corresponding files in the source code? (then I could track to check the changes on github).

Best regards,

Thomas

--
Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21

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