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ome / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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Ventana: Physical Size not being read #3416

Closed dgault closed 4 years ago

dgault commented 5 years ago

This issue was first raised in https://forum.image.sc/t/missing-metadata-for-ventana-images-in-qupath-with-bio-formats/28123

A sample file is available in QA-27763 and reproduces the issue.

From debugging it seems that most of our Ventana samples have the XML on ifd 2 which is the first resolution (0 and 1 being a label and thumbnail) - https://github.com/ome/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/VentanaReader.java#L460. For the provided QA there is no XML tag present on this ifd, but instead on ifd 0.

dgault commented 4 years ago

Resolved by https://github.com/ome/bioformats/pull/3494

imagesc-bot commented 3 years ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/bio-formats-read-region-equivalent/39150/13