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Commits an alternative Zeiss CZI Reader #4092

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Commits on Sep 8, 2023

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Commits on Nov 2, 2023

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Commits on Nov 16, 2023

  1. Fix initFile failures

    Small changes to fix some initFile failures
    dgault authored Nov 16, 2023
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  2. Fix initFile failure when unitsLength is reference frame

    zStep is always initialised as micrometer so no need to attempt unit conversion
    dgault authored Nov 16, 2023
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Commits on Dec 16, 2023

  1. CZI reader: fixes incorrect optimisation

    checks that a single sublock exists when a cropped plane matches exactly a subblock region
    NicoKiaru committed Dec 16, 2023
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Commits on Dec 17, 2023

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Commits on Dec 18, 2023

  1. Fix truncation issue in downsampling calculation

    Adds toString method to directory entry
    NicoKiaru committed Dec 18, 2023
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Commits on Jan 4, 2024

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  3. Recovers file reading when subblock metadata has been deleted but is …

    …present as an orphan block at the end of the file.
    NicoKiaru committed Jan 4, 2024
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Commits on Feb 4, 2024

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  2. Fis issue with CZI edge cases:

    - Fix mismatch between decompressed JPEGXR image dimension and subblock storedSize X & Y
    - Proper reading of linescans (handling of subblocks containing multiple Z or Ts)
    - Fix unit issue with linescans
    - Avoids NPE issue when no scaling metadata is found
    - adapts to PALM: make sure the data opens (downscaling can go below 1: superresolution)
    - Make metadata reading robust with absence of some sub-blocks
    - Correctly counts the number of channels, slices, and timepoints (they should always start at 0)
    - be robust to absence of sub-directory segment
    - There may be some information in slide previews that we do not want to keep. Hence a DummyMetadata is used when reading slide preview and macro images
    Minor documentation and formatting changes
    NicoKiaru committed Feb 4, 2024
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Commits on Feb 13, 2024

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Commits on Feb 22, 2024

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  2. Update ZeissCZIReader.java

    dgault authored Feb 22, 2024
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Commits on Feb 23, 2024

  1. Update ZeissCZIReader.java

    Attempt to close open file handles
    dgault authored Feb 23, 2024
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Commits on Jun 27, 2024

  1. Merge upstream

    NicoKiaru committed Jun 27, 2024
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