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Explained metadata differences between ZeissQuickStartCZIReader and ZeissCZI Reader

Rule #1 IMPROVEMENT

The quick reader reads the czi stage label name, instead of iterating scene indices. This fits better with the original CZI file.

Affected images:

  • (x 2) S=1_3x3_T=3_Z=4_CH=2.czi.autoStitch.true
  • (x 1) PALM_OnlineVerrechnet.czi.autoStitch.false
  • (x 264) 2023_11_30__RecognizedCode-27.czi.autoStitch.false
  • (x 1) S=1_CH=2.czi.autoStitch.true
  • (x 1) Z=5_CH=2.czi.autoStitch.true
  • (x 6) 2023_11_30__RecognizedCode-27.czi.autoStitch.true
  • (x 9) S=1_3x3_T=3_Z=4_CH=2.czi.autoStitch.false
  • (x 1) T=2_Z=5_CH=2.czi.autoStitch.false
  • (x 31) Demo LISH 4x8 15pct 647.czi.autoStitch.false
  • (x 90) W96_B2+B4_S=2_T=1=Z=1_C=1_Tile=5x9.czi.autoStitch.false
  • (x 1) S=1_CH=2.czi.autoStitch.false
  • (x 1) Plate1-Blue-A-12-Scene-3-P3-F2-03.czi.autoStitch.true
  • (x 5) S=3_1Pos_2Mosaic_T=2=Z=3_CH=2.czi.autoStitch.true
  • (x 184) v.zanotelli_20190509_p165_031.czi.autoStitch.false
  • (x 264) 2023_11_30__RecognizedCode-27-Background subtraction-08.czi.autoStitch.false
  • (x 2) split_hcr_probes_plasmid_pos_fov_tile3_Airyscan_Processing_Stitch.czi.autoStitch.true
  • (x 6) W96_B2+B4_S=2_T=1=Z=1_C=1_Tile=5x9.czi.autoStitch.true
  • (x 18) S=2_3x3_T=1_Z=4_CH=2.czi.autoStitch.false
  • (x 5) 3Dexample.czi.autoStitch.false
  • (x 6) 2023_11_30__RecognizedCode-27-Deconvolution (defaults)-11.czi.autoStitch.true
  • (x 4) S=2_2x2_T=1_Z=4_CH=1.czi.autoStitch.true
  • (x 1) MouseBrain_41Slices_1Tile_1Channel_2Illuminations_2Angles.czi.autoStitch.false
  • (x 1) T=3_CH=2.czi.autoStitch.false
  • (x 1) T=3_CH=2.czi.autoStitch.true
  • (x 35) test_gray.czi.autoStitch.false
  • (x 99) test-plate.czi.autoStitch.true
  • (x 1) PALM_OnlineVerrechnet.czi.autoStitch.true
  • (x 4) S=2_3x3_T=1_Z=4_CH=2.czi.autoStitch.true
  • (x 1) MouseBrain_41Slices_1Tile_3Channel_2Illuminations_2Angles.czi.autoStitch.true
  • (x 1) Z=5_CH=2.czi.autoStitch.false
  • (x 1) Palm_mitDrift.czi.autoStitch.false
  • (x 15) v.zanotelli_20190509_p165_031.czi.autoStitch.true
  • (x 2) S=2_T=3_CH=1.czi.autoStitch.false
  • (x 2) S=2_T=3_CH=1.czi.autoStitch.true
  • (x 18) S=2_3x3_T=3_CH=2.czi.autoStitch.false
  • (x 1) T=1_CH=2.czi.autoStitch.true
  • (x 8) S=2_2x2_T=3_Z=4_CH=1.czi.autoStitch.false
  • (x 4) Intestine_3color_RAC.czi.autoStitch.true
  • (x 1) T=3_Z=5_CH=2.czi.autoStitch.true
  • (x 1) MouseBrain_41Slices_1Tile_1Channel_2Illuminations_2Angles.czi.autoStitch.true
  • (x 1) Plate1-Blue-A-12-Scene-3-P3-F2-03.czi.autoStitch.false
  • (x 1) Palm_mitDrift.czi.autoStitch.true
  • (x 6) 2023_11_30__RecognizedCode-27-Background subtraction-08.czi.autoStitch.true
  • (x 2) S=2_T=3_Z=5_CH=1.czi.autoStitch.true
  • (x 45) S=3_1Pos_2Mosaic_T=2=Z=3_CH=2.czi.autoStitch.false
  • (x 6) W96_B2+B4_S=2_T=2=Z=4_C=3_Tile=5x9.czi.autoStitch.true
  • (x 5) Kidney_RAC_3color.czi.autoStitch.true
  • (x 2) S=2_T=3_Z=5_CH=1.czi.autoStitch.false
  • (x 8) S=2_2x2_T=1_Z=4_CH=1.czi.autoStitch.false
  • (x 4) S=2_2x2_T=3_Z=4_CH=1.czi.autoStitch.true
  • (x 8) S=2_2x2_Z=4_CH=1.czi.autoStitch.false
  • (x 30) Intestine_3color_RAC.czi.autoStitch.false
  • (x 8) S=2_2x2_T=3_CH=1.czi.autoStitch.false
  • (x 3) MouseBrain_41Slices_2x2Tiles_3Channels_2Illuminations_1Angle.czi.autoStitch.false
  • (x 4) S=2_2x2_Z=4_CH=1.czi.autoStitch.true
  • (x 48) Kidney_RAC_3color.czi.autoStitch.false
  • (x 1) T=1_CH=2.czi.autoStitch.false
  • (x 1) T=2_Z=5_CH=2.czi.autoStitch.true
  • (x 90) W96_B2+B4_S=2_T=2=Z=4_C=3_Tile=5x9.czi.autoStitch.false
  • (x 3) S=3_CH=2.czi.autoStitch.false
  • (x 1) MouseBrain_41Slices_1Tile_3Channel_2Illuminations_2Angles.czi.autoStitch.false
  • (x 3) Image_1_2023_08_18__14_32_31_964.czi.autoStitch.false
  • (x 4) S=2_2x2_CH=1.czi.autoStitch.true
  • (x 1) T=3_Z=5_CH=2.czi.autoStitch.false
  • (x 8) S=2_2x2_CH=1.czi.autoStitch.false
  • (x 3) S=3_CH=2.czi.autoStitch.true
  • (x 4) S=2_2x2_T=3_CH=1.czi.autoStitch.true
  • (x 18) S=2_3x3_T=3_Z=1_CH=2.czi.autoStitch.false
  • (x 4) S=2_3x3_T=3_CH=2.czi.autoStitch.true
  • (x 4) S=2_3x3_T=3_Z=1_CH=2.czi.autoStitch.true
  • (x 264) 2023_11_30__RecognizedCode-27-Deconvolution (defaults)-11.czi.autoStitch.false
  • (x 99) test-plate.czi.autoStitch.false

Rule #2 IMPROVEMENT

The quick reader reads the Z location correctly, and not the original reader.

Affected images:

  • (x 2499) RBC_full_time_series.czi.autoStitch.false
  • (x 20) Plate1-Blue-A-12-Scene-3-P3-F2-03.czi.autoStitch.true
  • (x 833) RBC_tiny.czi.autoStitch.false
  • (x 833) RBC_full_one_timepoint.czi.autoStitch.false
  • (x 4165) RBC_medium_LLSZ.czi.autoStitch.false
  • (x 2499) RBC_full_time_series.czi.autoStitch.true
  • (x 4165) RBC_medium_LLSZ.czi.autoStitch.true
  • (x 833) RBC_tiny.czi.autoStitch.true
  • (x 20) Plate1-Blue-A-12-Scene-3-P3-F2-03.czi.autoStitch.false
  • (x 833) RBC_full_one_timepoint.czi.autoStitch.true

Rule #3 IMPROVEMENT

The quick reader reads correctly the physical pixel for the lower resolution levels, in contrast to the original reader, which sets the same pixel size for all resolution levels (the one of the highest resolution).

Affected images:

  • (x 4) S=2_2x2_T=1_Z=4_CH=1.czi.autoStitch.true
  • (x 46) S=3_1Pos_2Mosaic_T=2=Z=3_CH=2.czi.autoStitch.false
  • (x 8) W96_B2+B4_S=2_T=2=Z=4_C=3_Tile=5x9.czi.autoStitch.true
  • (x 4) S=3_1Pos_2Mosaic_T=2=Z=3_CH=2.czi.autoStitch.true
  • (x 4) S=2_2x2_T=3_CH=1.czi.autoStitch.true
  • (x 8) W96_B2+B4_S=2_T=1=Z=1_C=1_Tile=5x9.czi.autoStitch.true
  • (x 4) S=2_3x3_T=1_Z=4_CH=2.czi.autoStitch.true
  • (x 4) S=2_3x3_T=3_CH=2.czi.autoStitch.true
  • (x 4) S=2_3x3_T=3_Z=1_CH=2.czi.autoStitch.true
  • (x 4) S=2_2x2_T=3_Z=4_CH=1.czi.autoStitch.true
  • (x 4) S=2_2x2_Z=4_CH=1.czi.autoStitch.true
  • (x 4) S=2_2x2_CH=1.czi.autoStitch.true

Rule #4 IMPROVEMENT

getPlaneDeltaT returns a wrong value (timestamp from first series) for the lower resolution levels in the original reader

Affected images:

  • (x 21) S=1_3x3_T=3_Z=4_CH=2.czi.autoStitch.true
  • (x 7) S=2_2x2_T=1_Z=4_CH=1.czi.autoStitch.true
  • (x 216) S=3_1Pos_2Mosaic_T=2=Z=3_CH=2.czi.autoStitch.false
  • (x 92) W96_B2+B4_S=2_T=2=Z=4_C=3_Tile=5x9.czi.autoStitch.true
  • (x 15) S=2_3x3_T=1_Z=4_CH=2.czi.autoStitch.true
  • (x 21) S=2_2x2_T=3_Z=4_CH=1.czi.autoStitch.true
  • (x 1) S=2_2x2_CH=1.czi.autoStitch.true
  • (x 22) S=3_1Pos_2Mosaic_T=2=Z=3_CH=2.czi.autoStitch.true
  • (x 3) S=2_2x2_T=3_CH=1.czi.autoStitch.true
  • (x 2) W96_B2+B4_S=2_T=1=Z=1_C=1_Tile=5x9.czi.autoStitch.true
  • (x 9) S=2_3x3_T=3_CH=2.czi.autoStitch.true
  • (x 9) S=2_3x3_T=3_Z=1_CH=2.czi.autoStitch.true
  • (x 7) S=2_2x2_Z=4_CH=1.czi.autoStitch.true

Rule #5 IDENTICAL

Metadata not present for modulo planes in original reader

Affected images:

  • (x 3255) 2021-02-25-tulip_unprocessed-Airyscan.czi.autoStitch.true
  • (x 3255) 2021-02-25-tulip_unprocessed-Airyscan.czi.autoStitch.false

Rule #6 IMPROVEMENT

The stage label is null in the original reader.

Affected images:

  • (x 31) Demo LISH 4x8 15pct 647.czi.autoStitch.false
  • (x 3) Image_1_2023_08_18__14_32_31_964.czi.autoStitch.false

Rule #7 IDENTICAL

When the pixel size is not defined (label / overview), the stage and plane location is in reference frame in the quick reader, and in micrometer in the original reader.

Affected images:

  • (x 4) v.zanotelli_20190509_p165_031_pt1.czi.autoStitch.true
  • (x 4) v.zanotelli_20190509_p165_031_pt1.czi.autoStitch.false

Rule #8 ISSUE

An edge case when the pixel size in Z is not defined, so one has to add a 0 in reference frame unit and a micrometer value in the metadata. The new reader chooses to set this operation as null, while the original reader keeps the micrometer value only

Affected images:

  • (x 2) v.zanotelli_20190509_p165_031_pt1.czi.autoStitch.true
  • (x 2) v.zanotelli_20190509_p165_031_pt1.czi.autoStitch.false

Rule #9 IDENTICAL

The quick reader sets the plane location as 0 micrometer, while the original reader sets it as 0 in reference frame unit.

Affected images:

  • (x 4) v.zanotelli_20190509_p165_031_pt2.czi.autoStitch.false
  • (x 4) v.zanotelli_20190509_p165_031_pt2.czi.autoStitch.true

Rule #10 IDENTICAL

A constant shift in XY (40 nm) that is below half a pixel (100 nm),

Affected images:

  • (x 40) S=2_2x2_T=1_Z=4_CH=1.czi.autoStitch.true
  • (x 16) S=2_2x2_CH=1.czi.autoStitch.false
  • (x 32) S=2_2x2_T=3_CH=1.czi.autoStitch.false
  • (x 104) S=2_2x2_T=3_Z=4_CH=1.czi.autoStitch.false
  • (x 32) S=2_2x2_T=3_CH=1.czi.autoStitch.true
  • (x 40) S=2_2x2_T=1_Z=4_CH=1.czi.autoStitch.false
  • (x 104) S=2_2x2_T=3_Z=4_CH=1.czi.autoStitch.true
  • (x 40) S=2_2x2_Z=4_CH=1.czi.autoStitch.false
  • (x 40) S=2_2x2_Z=4_CH=1.czi.autoStitch.true
  • (x 16) S=2_2x2_CH=1.czi.autoStitch.true

Rule #11 IMPROVEMENT

The original reader is not consistent when setting the plane positions: it returns the top left corner of all images, except when a plane contains many blocks (mosaic) and autostitching is set to true: in this case the original reader return the center location of the image. In comparison, the quick reader consistently returns the top left corner of the image, whether autostitch is true or false.

Affected images:

  • (x 100) S=1_3x3_T=3_Z=4_CH=2.czi.autoStitch.true
  • (x 40) S=2_2x2_T=1_Z=4_CH=1.czi.autoStitch.true
  • (x 671) S=3_1Pos_2Mosaic_T=2=Z=3_CH=2.czi.autoStitch.false
  • (x 300) W96_B2+B4_S=2_T=2=Z=4_C=3_Tile=5x9.czi.autoStitch.true
  • (x 166) MouseBrain_41Slices_1Tile_1Channel_2Illuminations_2Angles.czi.autoStitch.false
  • (x 72) S=2_3x3_T=1_Z=4_CH=2.czi.autoStitch.true
  • (x 494) MouseBrain_41Slices_1Tile_3Channel_2Illuminations_2Angles.czi.autoStitch.false
  • (x 40) S=2_2x2_T=1_Z=4_CH=1.czi.autoStitch.false
  • (x 104) S=2_2x2_T=3_Z=4_CH=1.czi.autoStitch.true
  • (x 494) MouseBrain_41Slices_1Tile_3Channel_2Illuminations_2Angles.czi.autoStitch.true
  • (x 40) S=2_2x2_Z=4_CH=1.czi.autoStitch.false
  • (x 494) MouseBrain_41Slices_2x2Tiles_3Channels_2Illuminations_1Angle.czi.autoStitch.true
  • (x 130) S=3_1Pos_2Mosaic_T=2=Z=3_CH=2.czi.autoStitch.true
  • (x 32) S=2_2x2_T=3_CH=1.czi.autoStitch.false
  • (x 104) S=2_2x2_T=3_Z=4_CH=1.czi.autoStitch.false
  • (x 1976) MouseBrain_41Slices_2x2Tiles_3Channels_2Illuminations_1Angle.czi.autoStitch.false
  • (x 32) S=2_2x2_T=3_CH=1.czi.autoStitch.true
  • (x 24) W96_B2+B4_S=2_T=1=Z=1_C=1_Tile=5x9.czi.autoStitch.true
  • (x 166) MouseBrain_41Slices_1Tile_1Channel_2Illuminations_2Angles.czi.autoStitch.true
  • (x 56) S=2_3x3_T=3_CH=2.czi.autoStitch.true
  • (x 56) S=2_3x3_T=3_Z=1_CH=2.czi.autoStitch.true
  • (x 40) S=2_2x2_Z=4_CH=1.czi.autoStitch.true

Table

OK File Name AutoStitch #Diffs
(Critical)		 #Diffs #Diffs Ignored #DiffsPixels Mem Gain Init Time Gain Read Time Gain
[Demo LISH 4x8 15pct 647.czi](compare/Demo LISH 4x8 15pct 647.flat_true.stitch_false.md) false 0 5384 62 0 3.2 0.2 0.7
[Demo LISH 4x8 15pct 647.czi](compare/Demo LISH 4x8 15pct 647.flat_true.stitch_true.md) true 0 114 0 0 11.4 2.1 0.9
✓ test_gray.czi false 0 0 35 0 1.4 0.4 1.0
✓ test_gray.czi true 0 0 0 0 2.5 1.2 0.8
Image_1_2023_08_18__14_32_31_964.czi false 0 19 6 0 1.6 0.8 1.0
Image_1_2023_08_18__14_32_31_964.czi true 0 4 0 0 1.7 1.0 1.0
test-plate.czi false 0 495 99 0 1.3 0.3 1.1
test-plate.czi true 0 495 99 0 1.3 0.5 1.0
✓ P1.czi false 0 0 0 0 1.8 0.3 1.1
✓ P1.czi true 0 0 0 0 1.8 0.9 1.3
✓ 2021-02-25-tulip_Airyscan.czi false 0 0 0 0 1.7 0.5 1.0
✓ 2021-02-25-tulip_Airyscan.czi true 0 0 0 0 1.7 1.0 1.2
✓ 2021-02-25-tulip_unprocessed-Airyscan.czi false 0 0 3255 0 2.1 3.1 0.9
✓ 2021-02-25-tulip_unprocessed-Airyscan.czi true 0 0 3255 0 2.1 0.9 0.9
✓ [Airyscan Lines Pattern.czi](compare/Airyscan Lines Pattern.flat_true.stitch_false.md) false 0 0 0 0 1.6 1.0 1.1
✓ [Airyscan Lines Pattern.czi](compare/Airyscan Lines Pattern.flat_true.stitch_true.md) true 0 0 0 0 1.6 1.0 1.2
✓ [Confocal Lines Pattern.czi](compare/Confocal Lines Pattern.flat_true.stitch_false.md) false 0 0 0 0 1.6 1.0 1.2
✓ [Confocal Lines Pattern.czi](compare/Confocal Lines Pattern.flat_true.stitch_true.md) true 0 0 0 0 1.6 1.0 1.2
✓ S=1_3x3_T=3_Z=4_CH=2.czi false 0 0 9 0 1.4 0.4 1.0
S=1_3x3_T=3_Z=4_CH=2.czi true 0 27 123 0 1.4 1.3 1.2
✓ S=1_CH=2.czi false 0 0 1 0 1.3 1.4 1.2
✓ S=1_CH=2.czi true 0 0 1 0 1.3 1.5 1.3
✓ S=2_2x2_CH=1.czi false 0 0 24 0 1.3 0.8 2.2
S=2_2x2_CH=1.czi true 0 4 25 0 1.3 0.9 1.4
✓ S=2_2x2_T=1_Z=4_CH=1.czi false 0 0 48 0 1.3 0.7 1.2
S=2_2x2_T=1_Z=4_CH=1.czi true 0 10 55 0 1.3 1.0 1.2
✓ S=2_2x2_T=3_CH=1.czi false 0 0 40 0 1.3 0.8 1.2
S=2_2x2_T=3_CH=1.czi true 0 8 43 0 1.3 1.0 1.2
✓ S=2_2x2_T=3_Z=4_CH=1.czi false 0 0 112 0 1.3 0.6 1.3
S=2_2x2_T=3_Z=4_CH=1.czi true 0 26 133 0 1.3 1.1 1.2
✓ S=2_2x2_Z=4_CH=1.czi false 0 0 48 0 1.3 0.8 1.1
S=2_2x2_Z=4_CH=1.czi true 0 10 55 0 1.3 1.1 1.3
✓ S=2_3x3_T=1_Z=4_CH=2.czi false 0 0 18 0 1.3 0.5 1.0
S=2_3x3_T=1_Z=4_CH=2.czi true 0 18 95 0 1.4 1.2 1.2
✓ S=2_3x3_T=3_CH=2.czi false 0 0 18 0 1.3 0.5 1.0
S=2_3x3_T=3_CH=2.czi true 0 14 73 0 1.4 1.1 1.1
✓ S=2_3x3_T=3_Z=1_CH=2.czi false 0 0 18 0 1.3 0.5 1.0
S=2_3x3_T=3_Z=1_CH=2.czi true 0 14 73 0 1.4 1.1 1.1
✓ S=2_T=3_CH=1.czi false 0 0 2 0 1.3 0.8 1.1
✓ S=2_T=3_CH=1.czi true 0 0 2 0 1.3 1.1 1.1
✓ S=2_T=3_Z=5_CH=1.czi false 0 0 2 0 1.3 0.7 1.1
✓ S=2_T=3_Z=5_CH=1.czi true 0 0 2 0 1.3 0.9 0.9
S=3_1Pos_2Mosaic_T=2=Z=3_CH=2.czi false 116 925 978 404999 1.5 0.4 1.5
S=3_1Pos_2Mosaic_T=2=Z=3_CH=2.czi true 0 26 161 0 1.5 1.3 1.2
✓ S=3_CH=2.czi false 0 0 3 0 1.3 0.8 1.1
✓ S=3_CH=2.czi true 0 0 3 0 1.3 0.9 1.1
✓ T=1_CH=2.czi false 0 0 1 0 1.3 1.4 1.3
✓ T=1_CH=2.czi true 0 0 1 0 1.3 1.5 1.3
✓ T=1_Z=5_CH=1.czi false 0 0 0 0 1.3 0.8 1.1
✓ T=1_Z=5_CH=1.czi true 0 0 0 0 1.3 1.0 1.1
✓ T=2_CH=1.czi false 0 0 0 0 1.3 1.4 1.3
✓ T=2_CH=1.czi true 0 0 0 0 1.3 1.6 1.3
✓ T=2_Z=5_CH=1.czi false 0 0 0 0 1.3 0.9 1.1
✓ T=2_Z=5_CH=1.czi true 0 0 0 0 1.3 0.9 1.1
✓ T=2_Z=5_CH=2.czi false 0 0 1 0 1.3 0.8 1.1
✓ T=2_Z=5_CH=2.czi true 0 0 1 0 1.3 0.9 1.1
✓ T=3_CH=2.czi false 0 0 1 0 1.3 0.9 1.1
✓ T=3_CH=2.czi true 0 0 1 0 1.3 1.0 1.2
✓ T=3_Z=5_CH=2.czi false 0 0 1 0 1.3 0.7 1.1
✓ T=3_Z=5_CH=2.czi true 0 0 1 0 1.3 0.9 1.2
✓ W96_B2+B4_S=2_T=1=Z=1_C=1_Tile=5x9.czi false 0 0 90 0 1.3 0.4 1.1
W96_B2+B4_S=2_T=1=Z=1_C=1_Tile=5x9.czi true 0 8 40 0 1.4 0.9 1.1
✓ W96_B2+B4_S=2_T=2=Z=4_C=3_Tile=5x9.czi false 0 0 90 0 1.9 0.3 1.1
W96_B2+B4_S=2_T=2=Z=4_C=3_Tile=5x9.czi true 0 100 406 0 2.5 3.0 1.2
✓ Z=5_CH=1.czi false 0 0 0 0 1.3 0.9 0.9
✓ Z=5_CH=1.czi true 0 0 0 0 1.3 1.0 1.0
✓ Z=5_CH=2.czi false 0 0 1 0 1.3 0.9 0.9
✓ Z=5_CH=2.czi true 0 0 1 0 1.3 1.0 1.0
✓ RBC_full_one_timepoint.czi false 0 0 833 0 1.7 10.3 1.5
✓ RBC_full_one_timepoint.czi true 0 0 833 0 1.7 3.0 1.5
✓ RBC_full_time_series.czi false 0 0 2499 0 2.1 21.8 2.0
✓ RBC_full_time_series.czi true 0 0 2499 0 2.1 5.0 2.0
✓ RBC_medium_LLSZ.czi false 0 0 4165 0 2.2 27.2 2.1
✓ RBC_medium_LLSZ.czi true 0 0 4165 0 2.2 6.2 2.2
✓ RBC_tiny.czi false 0 0 833 0 1.7 11.0 1.6
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