├── .github └── workflows │ ├── maven_deployment_and_pm_update.yml │ ├── ndtiff_tests.yml │ └── update_pypi.yml ├── .gitignore ├── LICENSE ├── README.md ├── java ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── micromanager │ │ └── ndtiffstorage │ │ ├── DisplaySettingsWriter.java │ │ ├── EssentialImageMetadata.java │ │ ├── ImageWrittenListener.java │ │ ├── IndexEntryData.java │ │ ├── IndexWriter.java │ │ ├── MultiresNDTiffAPI.java │ │ ├── NDRAMStorage.java │ │ ├── NDTiffAPI.java │ │ ├── NDTiffReader.java │ │ ├── NDTiffStorage.java │ │ ├── NDTiffWriter.java │ │ ├── ResolutionLevel.java │ │ ├── SpeedTest.java │ │ ├── StorageMD.java │ │ ├── Test.java │ │ └── VERSION.java │ └── test │ └── java │ └── org │ └── micromanager │ └── ndtiffstorage │ └── test │ └── LoadDataTest.java ├── python ├── LICENSE ├── README.md ├── ndstorage │ ├── __init__.py │ ├── _superclass.py │ ├── _version.py │ ├── file_io.py │ ├── ndram_dataset.py │ ├── ndstorage_base.py │ ├── ndtiff_dataset.py │ ├── ndtiff_file.py │ ├── ndtiff_index.py │ ├── ndtiff_pyramid_dataset.py │ ├── old_format_version_readers │ │ ├── __init__.py │ │ ├── nd_tiff_v2.py │ │ └── ndtiff_v1.py │ └── test │ │ ├── __init__.py │ │ ├── conftest.py │ │ ├── data_loading_test.py │ │ ├── test_custom_io.py │ │ ├── write_speed_test.py │ │ └── writing_test.py ├── package.sh ├── pyproject.toml └── tmp.txt └── test_data ├── v2 ├── ndtiffv2.0_stitched_test │ ├── Downsampled_x16 │ │ ├── NDTiff.index │ │ └── ndtiffv2.0_stitched_test_NDTiffStack.tif │ ├── Downsampled_x2 │ │ ├── NDTiff.index │ │ └── ndtiffv2.0_stitched_test_NDTiffStack.tif │ ├── Downsampled_x4 │ │ ├── NDTiff.index │ │ └── ndtiffv2.0_stitched_test_NDTiffStack.tif │ ├── Downsampled_x8 │ │ ├── NDTiff.index │ │ └── ndtiffv2.0_stitched_test_NDTiffStack.tif │ ├── Full resolution │ │ ├── NDTiff.index │ │ └── ndtiffv2.0_stitched_test_NDTiffStack.tif │ └── display_settings.txt └── ndtiffv2.0_test │ ├── Full resolution │ ├── NDTiff.index │ └── ndtiffv2.0_test_NDTiffStack.tif │ └── display_settings.txt └── v3 ├── 12_bit_pycromanager_mda ├── 12_bit_pycromanager_mda_NDTiffStack.tif ├── NDTiff.index └── display_settings.txt ├── Magellan_expolore_multi_channel ├── Downsampled_x128 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x16 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x2 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x256 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x32 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x4 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x512 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x64 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x8 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Full resolution │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index └── display_settings.txt ├── Magellan_expolore_negative_indices_and_overwritten ├── Downsampled_x1024 │ ├── Magellan_expolore_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x128 │ ├── Magellan_expolore_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x16 │ ├── Magellan_expolore_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x2 │ ├── Magellan_expolore_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x256 │ ├── Magellan_expolore_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x32 │ ├── Magellan_expolore_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x4 │ ├── Magellan_expolore_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x512 │ ├── Magellan_expolore_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x64 │ ├── Magellan_expolore_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x8 │ ├── Magellan_expolore_NDTiffStack.tif │ └── NDTiff.index ├── Full resolution │ ├── Magellan_expolore_NDTiffStack.tif │ └── NDTiff.index └── display_settings.txt ├── Nonstandard_axis_names ├── NDTiff.index ├── display_settings.txt └── l_axis_NDTiffStack.tif ├── labeled_positions_1 ├── NDTiff.index └── labeled_positions_NDTiffStack.tif ├── mm_mda_tcz_15 ├── DisplaySettings.json ├── NDTiff.index └── mm_mda_tcz_15_NDTiffStack.tif ├── ndtiff3.2_11bit_1 ├── NDTiff.index └── ndtiff3.2_11bit_NDTiffStack.tif ├── ndtiff3.2_magellan_explore_rgb ├── Downsampled_x16 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x2 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x32 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x4 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Downsampled_x8 │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index ├── Full resolution │ ├── Magellan_expolore_multi_channel_NDTiffStack.tif │ └── NDTiff.index └── display_settings.txt ├── ndtiff3.2_monochrome ├── NDTiff.index ├── NDTiff3.2_monochrome_NDTiffStack.tif └── display_settings.txt ├── ndtiff3.2_multichannel ├── NDTiff.index ├── NDTiff3.2_multichannel_NDTiffStack.tif └── display_settings.txt ├── ndtiffv3.0_stitched_test ├── Downsampled_x16 │ ├── NDTiff.index │ └── ndtiffv3.0_stitched_test_NDTiffStack.tif ├── Downsampled_x2 │ ├── NDTiff.index │ └── ndtiffv3.0_stitched_test_NDTiffStack.tif ├── Downsampled_x4 │ ├── NDTiff.index │ └── ndtiffv3.0_stitched_test_NDTiffStack.tif ├── Downsampled_x8 │ ├── NDTiff.index │ └── ndtiffv3.0_stitched_test_NDTiffStack.tif ├── Full resolution │ ├── NDTiff.index │ └── ndtiffv3.0_stitched_test_NDTiffStack.tif └── display_settings.txt ├── ndtiffv3.0_test ├── NDTiff.index ├── display_settings.txt └── ndtiffv3.0_test_NDTiffStack.tif ├── no_magellan_explore_multi_channel ├── Downsampled_x16 │ ├── NDTiff.index │ └── explore_channels_NDTiffStack.tif ├── Downsampled_x2 │ ├── NDTiff.index │ └── explore_channels_NDTiffStack.tif ├── Downsampled_x32 │ ├── NDTiff.index │ └── explore_channels_NDTiffStack.tif ├── Downsampled_x4 │ ├── NDTiff.index │ └── explore_channels_NDTiffStack.tif ├── Downsampled_x64 │ ├── NDTiff.index │ └── explore_channels_NDTiffStack.tif ├── Downsampled_x8 │ ├── NDTiff.index │ └── explore_channels_NDTiffStack.tif ├── Full resolution │ ├── NDTiff.index │ └── explore_channels_NDTiffStack.tif └── display_settings.txt ├── no_magellan_explore_no_channel ├── Downsampled_x128 │ ├── NDTiff.index │ └── explore_no_channels_NDTiffStack.tif ├── Downsampled_x16 │ ├── NDTiff.index │ └── explore_no_channels_NDTiffStack.tif ├── Downsampled_x2 │ ├── NDTiff.index │ └── explore_no_channels_NDTiffStack.tif ├── Downsampled_x32 │ ├── NDTiff.index │ └── explore_no_channels_NDTiffStack.tif ├── Downsampled_x4 │ ├── NDTiff.index │ └── explore_no_channels_NDTiffStack.tif ├── Downsampled_x64 │ ├── NDTiff.index 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