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Expand use of subfile type tags#145

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sbesson merged 1 commit intoglencoesoftware:masterfrom
melissalinkert:legacy-subfiletype
Nov 19, 2025
Merged

Expand use of subfile type tags#145
sbesson merged 1 commit intoglencoesoftware:masterfrom
melissalinkert:legacy-subfiletype

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@melissalinkert melissalinkert commented Oct 14, 2025

See pages 36 and 40-41 of https://www.itu.int/itudoc/itu-t/com16/tiff-fx/docs/tiff6.pdf.

This is an attempt at improving compatibility with other tools (e.g. Openslide) when using the --legacy option, and not intended to impact use of Bio-Formats/OMERO.

tiffinfo or tiffdump without this change on a file converted with --legacy should show that neither subfile tag was being written. When converting with this change and the same options, both subfile tags should be written for every IFD.

mabruce
mabruce approved these changes Oct 20, 2025
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This PR appears to work as expected. Tested with an isyntax image converted to OME-NGFF with isyntax2raw write_tiles --linear16to8 True file.isyntax file.zarr, and then converted to a legacy pyramid with this PR: raw2ometiff file.zarr file.legacy.tiff --legacy --rgb --compression JPEG.

OpenSlide Python now recognizes the expected number of pyramid levels, whereas previously on 1 level was reported:

>>> import openslide
>>> s = openslide.OpenSlide('file.legacy.tiff')
>>> s.properties['openslide.level-count']
'9'
$ tiffinfo file.legacy.tiff
TIFF Directory at offset 0x394219536 (177f5010)
  Subfile Type: (0 = 0x0)
  Image Width: 179999 Image Length: 85112
  Tile Width: 512 Tile Length: 512
  Resolution: 40290.4, 40290.4 pixels/cm
  Bits/Sample: 8
  Sample Format: unsigned integer
  Compression Scheme: JPEG
  Photometric Interpretation: RGB color
  Samples/Pixel: 3
  Planar Configuration: single image plane
  ImageDescription: <?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:94b98768-99a5-448b-a765-4765abfb7e3a" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Instrument ID="Instrument:0"><Objective ID="Objective:0:0" NominalMagnification="40.0"/></Instrument><Image ID="Image:0" Name="XXXXXXXX"><AcquisitionDate>2024-12-01T16:36:30.691</AcquisitionDate><Description>PHILIPS UFS B300 V2.1.0.14652 | Quality=2 | DWT=LeGall53 | Compressor=Hulsken2</Description><InstrumentRef ID="Instrument:0"/><ObjectiveSettings ID="Objective:0:0"/><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="0.2481982421875" PhysicalSizeXUnit="µm" PhysicalSizeY="0.2481982421875" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="3" SizeT="1" SizeX="179999" SizeY="85112" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="3"><LightPath/></Channel><TiffData IFD="0" PlaneCount="1"><UUID FileName="file.legacy.tiff">urn:uuid:94b98768-99a5-448b-a765-4765abfb7e3a</UUID></TiffData></Pixels></Image><Image ID="Image:1" Name="label image"><AcquisitionDate>2024-12-01T16:36:30.691</AcquisitionDate><InstrumentRef ID="Instrument:0"/><ObjectiveSettings ID="Objective:0:0"/><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:1" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="89997" SizeY="42554" SizeZ="1" Type="uint8"><Channel ID="Channel:1:0" SamplesPerPixel="3"><LightPath/></Channel></Pixels></Image><Image ID="Image:2" Name="macro image"><AcquisitionDate>2024-12-01T16:36:30.691</AcquisitionDate><InstrumentRef ID="Instrument:0"/><ObjectiveSettings ID="Objective:0:0"/><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:2" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="44996" SizeY="21274" SizeZ="1" Type="uint8"><Channel ID="Channel:2:0" SamplesPerPixel="3"><LightPath/></Channel></Pixels></Image><Image ID="Image:3"><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:3" SizeC="3" SizeT="1" SizeX="22496" SizeY="10635" SizeZ="1" Type="uint8"><Channel ID="Channel:3:0" SamplesPerPixel="3"><LightPath/></Channel></Pixels></Image><Image ID="Image:4"><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:4" SizeC="3" SizeT="1" SizeX="11246" SizeY="5315" SizeZ="1" Type="uint8"><Channel ID="Channel:4:0" SamplesPerPixel="3"><LightPath/></Channel></Pixels></Image><Image ID="Image:5"><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:5" SizeC="3" SizeT="1" SizeX="5621" SizeY="2655" SizeZ="1" Type="uint8"><Channel ID="Channel:5:0" SamplesPerPixel="3"><LightPath/></Channel></Pixels></Image><Image ID="Image:6"><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:6" SizeC="3" SizeT="1" SizeX="2808" SizeY="1325" SizeZ="1" Type="uint8"><Channel ID="Channel:6:0" SamplesPerPixel="3"><LightPath/></Channel></Pixels></Image><Image ID="Image:7"><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:7" SizeC="3" SizeT="1" SizeX="1402" SizeY="660" SizeZ="1" Type="uint8"><Channel ID="Channel:7:0" SamplesPerPixel="3"><LightPath/></Channel></Pixels></Image><Image ID="Image:8"><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:8" SizeC="3" SizeT="1" SizeX="699" SizeY="328" SizeZ="1" Type="uint8"><Channel ID="Channel:8:0" SamplesPerPixel="3"><LightPath/></Channel></Pixels></Image></OME>
  Software: Faas-raw2ometiff
TIFF Directory at offset 0x395164025 (178db979)
  Subfile Type: reduced-resolution image (1 = 0x1)
  Image Width: 89997 Image Length: 42554
  Tile Width: 512 Tile Length: 512
  Resolution: 40290.4, 40290.4 pixels/cm
  Bits/Sample: 8
  Sample Format: unsigned integer
  Compression Scheme: JPEG
  Photometric Interpretation: RGB color
  Samples/Pixel: 3
  Planar Configuration: single image plane
  Software: Faas-raw2ometiff
TIFF Directory at offset 0x395400962 (17915702)
  Subfile Type: reduced-resolution image (1 = 0x1)
  Image Width: 44996 Image Length: 21274
  Tile Width: 512 Tile Length: 512
  Resolution: 40290.4, 40290.4 pixels/cm
  Bits/Sample: 8
  Sample Format: unsigned integer
  Compression Scheme: JPEG
  Photometric Interpretation: RGB color
  Samples/Pixel: 3
  Planar Configuration: single image plane
  Software: Faas-raw2ometiff
TIFF Directory at offset 0x395460491 (17923f8b)
  Subfile Type: reduced-resolution image (1 = 0x1)
  Image Width: 22496 Image Length: 10635
  Tile Width: 512 Tile Length: 512
  Resolution: 40290.4, 40290.4 pixels/cm
  Bits/Sample: 8
  Sample Format: unsigned integer
  Compression Scheme: JPEG
  Photometric Interpretation: RGB color
  Samples/Pixel: 3
  Planar Configuration: single image plane
  Software: Faas-raw2ometiff
TIFF Directory at offset 0x395475668 (17927ad4)
  Subfile Type: reduced-resolution image (1 = 0x1)
  Image Width: 11246 Image Length: 5315
  Tile Width: 512 Tile Length: 512
  Resolution: 40290.4, 40290.4 pixels/cm
  Bits/Sample: 8
  Sample Format: unsigned integer
  Compression Scheme: JPEG
  Photometric Interpretation: RGB color
  Samples/Pixel: 3
  Planar Configuration: single image plane
  Software: Faas-raw2ometiff
TIFF Directory at offset 0x395479933 (17928b7d)
  Subfile Type: reduced-resolution image (1 = 0x1)
  Image Width: 5621 Image Length: 2655
  Tile Width: 512 Tile Length: 512
  Resolution: 40290.4, 40290.4 pixels/cm
  Bits/Sample: 8
  Sample Format: unsigned integer
  Compression Scheme: JPEG
  Photometric Interpretation: RGB color
  Samples/Pixel: 3
  Planar Configuration: single image plane
  Software: Faas-raw2ometiff
TIFF Directory at offset 0x395481382 (17929126)
  Subfile Type: reduced-resolution image (1 = 0x1)
  Image Width: 2808 Image Length: 1325
  Tile Width: 512 Tile Length: 512
  Resolution: 40290.4, 40290.4 pixels/cm
  Bits/Sample: 8
  Sample Format: unsigned integer
  Compression Scheme: JPEG
  Photometric Interpretation: RGB color
  Samples/Pixel: 3
  Planar Configuration: single image plane
  Software: Faas-raw2ometiff
TIFF Directory at offset 0x395482063 (179293cf)
  Subfile Type: reduced-resolution image (1 = 0x1)
  Image Width: 1402 Image Length: 660
  Tile Width: 512 Tile Length: 512
  Resolution: 40290.4, 40290.4 pixels/cm
  Bits/Sample: 8
  Sample Format: unsigned integer
  Compression Scheme: JPEG
  Photometric Interpretation: RGB color
  Samples/Pixel: 3
  Planar Configuration: single image plane
  Software: Faas-raw2ometiff
TIFF Directory at offset 0x395482552 (179295b8)
  Subfile Type: reduced-resolution image (1 = 0x1)
  Image Width: 699 Image Length: 328
  Tile Width: 512 Tile Length: 512
  Resolution: 40290.4, 40290.4 pixels/cm
  Bits/Sample: 8
  Sample Format: unsigned integer
  Compression Scheme: JPEG
  Photometric Interpretation: RGB color
  Samples/Pixel: 3
  Planar Configuration: single image plane
  Software: Faas-raw2ometiff

bftools-8.0.1-761/showinf correctly identifies this file as a "Pyramid TIFF".

The image imports into OMERO Plus without errors and the pyramid loads as expected in PathViewer.

sbesson
sbesson reviewed Oct 23, 2025
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I used the following script to generate OME-TIFF files across various layouts (single plane, multi plane, single plane with multiple samples/pixels) in both legacy and non-legacy mode:

./bioformats2raw-0.11.0/bin/bioformats2raw "test&sizeX=5000&sizeY=5000.fake" single_plane.zarr
./bioformats2raw-0.11.0/bin/bioformats2raw "test&sizeX=5000&sizeY=5000&sizeC=3.fake" 3channels.zarr
./bioformats2raw-0.11.0/bin/bioformats2raw "test&sizeX=5000&sizeY=5000&sizeC=3&rgb=3.fake" 3channels_rgb.zarr
mkdir raw2ometiff_0.8.0
./raw2ometiff-0.8.0/bin/raw2ometiff single_plane.zarr raw2ometiff_0.8.0/single_plane.ome.tiff
./raw2ometiff-0.8.0/bin/raw2ometiff single_plane.zarr raw2ometiff_0.8.0/single_plane_legacy.ome.tiff --legacy
./raw2ometiff-0.8.0/bin/raw2ometiff 3channels.zarr raw2ometiff_0.8.0/3channels.ome.tiff
./raw2ometiff-0.8.0/bin/raw2ometiff 3channels.zarr raw2ometiff_0.8.0/3channels_legacy.ome.tiff --legacy
./raw2ometiff-0.8.0/bin/raw2ometiff 3channels_rgb.zarr raw2ometiff_0.8.0/3channels_rgb.ome.tiff --rgb
./raw2ometiff-0.8.0/bin/raw2ometiff 3channels_rgb.zarr raw2ometiff_0.8.0/3channels_rgb_legacy.ome.tiff --rgb --legacy
mkdir raw2ometiff_0.9.0-SNAPSHOT
./raw2ometiff-0.9.0-SNAPSHOT/bin/raw2ometiff single_plane.zarr raw2ometiff_0.9.0-SNAPSHOT/single_plane.ome.tiff
./raw2ometiff-0.9.0-SNAPSHOT/bin/raw2ometiff single_plane.zarr raw2ometiff_0.9.0-SNAPSHOT/single_plane_legacy.ome.tiff --legacy
./raw2ometiff-0.9.0-SNAPSHOT/bin/raw2ometiff 3channels.zarr raw2ometiff_0.9.0-SNAPSHOT/3channels.ome.tiff
./raw2ometiff-0.9.0-SNAPSHOT/bin/raw2ometiff 3channels.zarr raw2ometiff_0.9.0-SNAPSHOT/3channels_legacy.ome.tiff --legacy
./raw2ometiff-0.9.0-SNAPSHOT/bin/raw2ometiff 3channels_rgb.zarr raw2ometiff_0.9.0-SNAPSHOT/3channels_rgb.ome.tiff --rgb
./raw2ometiff-0.9.0-SNAPSHOT/bin/raw2ometiff 3channels_rgb.zarr raw2ometiff_0.9.0-SNAPSHOT/3channels_rgb_legacy.ome.tiff --rgb --legacy

The diff between the output of tiffinfo of both folders is as follows

sbesson@Sebastien-GS-MacBook-Pro-2025 Downloads % diff 0.8.0.out 0.9.0-SNAPSHOT.out 
1c1
< File raw2ometiff_0.8.0/3channels_legacy.ome.tiff:
---
> File raw2ometiff_0.9.0-SNAPSHOT/3channels_legacy.ome.tiff:
3a4
>   Subfile Type: multi-page document (2 = 0x2)
13c14
<   ImageDescription: <?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:063968ea-3756-43ee-b60a-50e5b8ad6e7a" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="test"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="5000" SizeY="5000" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><TiffData IFD="0" PlaneCount="3"><UUID FileName="3channels_legacy.ome.tiff">urn:uuid:063968ea-3756-43ee-b60a-50e5b8ad6e7a</UUID></TiffData></Pixels></Image><Image ID="Image:1"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:1" SizeC="3" SizeT="1" SizeX="2500" SizeY="2500" SizeZ="1" Type="uint8"><Channel ID="Channel:1:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:1:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:1:2" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:2"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:2" SizeC="3" SizeT="1" SizeX="1250" SizeY="1250" SizeZ="1" Type="uint8"><Channel ID="Channel:2:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:2:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:2:2" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:3"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:3" SizeC="3" SizeT="1" SizeX="625" SizeY="625" SizeZ="1" Type="uint8"><Channel ID="Channel:3:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:3:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:3:2" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:4"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:4" SizeC="3" SizeT="1" SizeX="312" SizeY="312" SizeZ="1" Type="uint8"><Channel ID="Channel:4:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:4:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:4:2" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:5"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:5" SizeC="3" SizeT="1" SizeX="156" SizeY="156" SizeZ="1" Type="uint8"><Channel ID="Channel:5:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:5:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:5:2" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image></OME>
---
>   ImageDescription: <?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:17391953-25e5-4677-85ff-9a247760ad34" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="test"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="5000" SizeY="5000" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><TiffData IFD="0" PlaneCount="3"><UUID FileName="3channels_legacy.ome.tiff">urn:uuid:17391953-25e5-4677-85ff-9a247760ad34</UUID></TiffData></Pixels></Image><Image ID="Image:1"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:1" SizeC="3" SizeT="1" SizeX="2500" SizeY="2500" SizeZ="1" Type="uint8"><Channel ID="Channel:1:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:1:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:1:2" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:2"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:2" SizeC="3" SizeT="1" SizeX="1250" SizeY="1250" SizeZ="1" Type="uint8"><Channel ID="Channel:2:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:2:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:2:2" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:3"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:3" SizeC="3" SizeT="1" SizeX="625" SizeY="625" SizeZ="1" Type="uint8"><Channel ID="Channel:3:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:3:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:3:2" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:4"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:4" SizeC="3" SizeT="1" SizeX="312" SizeY="312" SizeZ="1" Type="uint8"><Channel ID="Channel:4:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:4:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:4:2" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:5"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:5" SizeC="3" SizeT="1" SizeX="156" SizeY="156" SizeZ="1" Type="uint8"><Channel ID="Channel:5:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:5:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:5:2" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image></OME>
17c18,19
< TIFF Directory at offset 0xecad2e (15510830)
---
> TIFF Directory at offset 0xecad56 (15510870)
>   Subfile Type: multi-page document (2 = 0x2)
30c32,33
< TIFF Directory at offset 0xecb01f (15511583)
---
> TIFF Directory at offset 0xecb06f (15511663)
>   Subfile Type: multi-page document (2 = 0x2)
43c46,47
< TIFF Directory at offset 0xecb310 (15512336)
---
> TIFF Directory at offset 0xecb388 (15512456)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
56c60,61
< TIFF Directory at offset 0xecb501 (15512833)
---
> TIFF Directory at offset 0xecb5a1 (15512993)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
69c74,75
< TIFF Directory at offset 0xecb6f2 (15513330)
---
> TIFF Directory at offset 0xecb7ba (15513530)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
82c88,89
< TIFF Directory at offset 0xecb8e3 (15513827)
---
> TIFF Directory at offset 0xecb9d3 (15514067)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
95c102,103
< TIFF Directory at offset 0xecba84 (15514244)
---
> TIFF Directory at offset 0xecbb9c (15514524)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
108c116,117
< TIFF Directory at offset 0xecbc25 (15514661)
---
> TIFF Directory at offset 0xecbd65 (15514981)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
121c130,131
< TIFF Directory at offset 0xecbdc6 (15515078)
---
> TIFF Directory at offset 0xecbf2e (15515438)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
134c144,145
< TIFF Directory at offset 0xecbf27 (15515431)
---
> TIFF Directory at offset 0xecc0b7 (15515831)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
147c158,159
< TIFF Directory at offset 0xecc088 (15515784)
---
> TIFF Directory at offset 0xecc240 (15516224)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
160c172,173
< TIFF Directory at offset 0xecc1e9 (15516137)
---
> TIFF Directory at offset 0xecc3c9 (15516617)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
173c186,187
< TIFF Directory at offset 0xecc34a (15516490)
---
> TIFF Directory at offset 0xecc552 (15517010)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
186c200,201
< TIFF Directory at offset 0xecc4ab (15516843)
---
> TIFF Directory at offset 0xecc6db (15517403)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
199c214,215
< TIFF Directory at offset 0xecc60c (15517196)
---
> TIFF Directory at offset 0xecc864 (15517796)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
212c228,229
< TIFF Directory at offset 0xecc76d (15517549)
---
> TIFF Directory at offset 0xecc9ed (15518189)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
225c242,243
< TIFF Directory at offset 0xecc8ce (15517902)
---
> TIFF Directory at offset 0xeccb76 (15518582)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
237c255
< File raw2ometiff_0.8.0/3channels_rgb_legacy.ome.tiff:
---
> File raw2ometiff_0.9.0-SNAPSHOT/3channels_rgb_legacy.ome.tiff:
239a258
>   Subfile Type: (0 = 0x0)
249c268
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< TIFF Directory at offset 0xecae44 (15511108)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 3 of chain 1 at offset 0xecaa0e (15510030):
> TIFF Directory at offset 0xecaef8 (15511288)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
872,874c899,901
< --- SubIFD 0 of chain 2 at offset 0xecab50 (15510352):
< TIFF Directory at offset 0xecab50 (15510352)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 0 of chain 2 at offset 0xecabdc (15510492):
> TIFF Directory at offset 0xecabdc (15510492)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
885,887c912,914
< --- SubIFD 1 of chain 2 at offset 0xecab50 (15510352):
< TIFF Directory at offset 0xecacca (15510730)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 1 of chain 2 at offset 0xecabdc (15510492):
> TIFF Directory at offset 0xecad6a (15510890)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
898,900c925,927
< --- SubIFD 2 of chain 2 at offset 0xecab50 (15510352):
< TIFF Directory at offset 0xecae44 (15511108)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 2 of chain 2 at offset 0xecabdc (15510492):
> TIFF Directory at offset 0xecaef8 (15511288)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
911,913c938,940
< --- SubIFD 0 of chain 3 at offset 0xecacca (15510730):
< TIFF Directory at offset 0xecacca (15510730)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 0 of chain 3 at offset 0xecad6a (15510890):
> TIFF Directory at offset 0xecad6a (15510890)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
924,926c951,953
< --- SubIFD 1 of chain 3 at offset 0xecacca (15510730):
< TIFF Directory at offset 0xecae44 (15511108)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 1 of chain 3 at offset 0xecad6a (15510890):
> TIFF Directory at offset 0xecaef8 (15511288)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
937,939c964,966
< --- SubIFD 0 of chain 4 at offset 0xecae44 (15511108):
< TIFF Directory at offset 0xecae44 (15511108)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 0 of chain 4 at offset 0xecaef8 (15511288):
> TIFF Directory at offset 0xecaef8 (15511288)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
952c979,980
< TIFF Directory at offset 0xecc300 (15516416)
---
> TIFF Directory at offset 0xecc47c (15516796)
>   Subfile Type: multi-page document (2 = 0x2)
962c990
<   SubIFD Offsets: 15511486 15512008 15512450 15512828 15513206
---
>   SubIFD Offsets: 15511686 15512228 15512690 15513088 15513486
965,967c993,995
< --- SubIFD 0 of chain 0 at offset 0xecafbe (15511486):
< TIFF Directory at offset 0xecafbe (15511486)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 0 of chain 0 at offset 0xecb086 (15511686):
> TIFF Directory at offset 0xecb086 (15511686)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
978,980c1006,1008
< --- SubIFD 1 of chain 0 at offset 0xecafbe (15511486):
< TIFF Directory at offset 0xecb1c8 (15512008)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 1 of chain 0 at offset 0xecb086 (15511686):
> TIFF Directory at offset 0xecb2a4 (15512228)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
991,993c1019,1021
< --- SubIFD 2 of chain 0 at offset 0xecafbe (15511486):
< TIFF Directory at offset 0xecb382 (15512450)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 2 of chain 0 at offset 0xecb086 (15511686):
> TIFF Directory at offset 0xecb472 (15512690)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1004,1006c1032,1034
< --- SubIFD 3 of chain 0 at offset 0xecafbe (15511486):
< TIFF Directory at offset 0xecb4fc (15512828)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 3 of chain 0 at offset 0xecb086 (15511686):
> TIFF Directory at offset 0xecb600 (15513088)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1017,1019c1045,1047
< --- SubIFD 4 of chain 0 at offset 0xecafbe (15511486):
< TIFF Directory at offset 0xecb676 (15513206)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 4 of chain 0 at offset 0xecb086 (15511686):
> TIFF Directory at offset 0xecb78e (15513486)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1030,1032c1058,1060
< --- SubIFD 0 of chain 1 at offset 0xecb1c8 (15512008):
< TIFF Directory at offset 0xecb1c8 (15512008)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 0 of chain 1 at offset 0xecb2a4 (15512228):
> TIFF Directory at offset 0xecb2a4 (15512228)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1043,1045c1071,1073
< --- SubIFD 1 of chain 1 at offset 0xecb1c8 (15512008):
< TIFF Directory at offset 0xecb382 (15512450)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 1 of chain 1 at offset 0xecb2a4 (15512228):
> TIFF Directory at offset 0xecb472 (15512690)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1056,1058c1084,1086
< --- SubIFD 2 of chain 1 at offset 0xecb1c8 (15512008):
< TIFF Directory at offset 0xecb4fc (15512828)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 2 of chain 1 at offset 0xecb2a4 (15512228):
> TIFF Directory at offset 0xecb600 (15513088)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1069,1071c1097,1099
< --- SubIFD 3 of chain 1 at offset 0xecb1c8 (15512008):
< TIFF Directory at offset 0xecb676 (15513206)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 3 of chain 1 at offset 0xecb2a4 (15512228):
> TIFF Directory at offset 0xecb78e (15513486)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1082,1084c1110,1112
< --- SubIFD 0 of chain 2 at offset 0xecb382 (15512450):
< TIFF Directory at offset 0xecb382 (15512450)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 0 of chain 2 at offset 0xecb472 (15512690):
> TIFF Directory at offset 0xecb472 (15512690)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1095,1097c1123,1125
< --- SubIFD 1 of chain 2 at offset 0xecb382 (15512450):
< TIFF Directory at offset 0xecb4fc (15512828)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 1 of chain 2 at offset 0xecb472 (15512690):
> TIFF Directory at offset 0xecb600 (15513088)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1108,1110c1136,1138
< --- SubIFD 2 of chain 2 at offset 0xecb382 (15512450):
< TIFF Directory at offset 0xecb676 (15513206)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 2 of chain 2 at offset 0xecb472 (15512690):
> TIFF Directory at offset 0xecb78e (15513486)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1121,1123c1149,1151
< --- SubIFD 0 of chain 3 at offset 0xecb4fc (15512828):
< TIFF Directory at offset 0xecb4fc (15512828)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 0 of chain 3 at offset 0xecb600 (15513088):
> TIFF Directory at offset 0xecb600 (15513088)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1134,1136c1162,1164
< --- SubIFD 1 of chain 3 at offset 0xecb4fc (15512828):
< TIFF Directory at offset 0xecb676 (15513206)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 1 of chain 3 at offset 0xecb600 (15513088):
> TIFF Directory at offset 0xecb78e (15513486)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1147,1149c1175,1177
< --- SubIFD 0 of chain 4 at offset 0xecb676 (15513206):
< TIFF Directory at offset 0xecb676 (15513206)
<   Subfile Type: reduced-resolution image (1 = 0x1)
---
> --- SubIFD 0 of chain 4 at offset 0xecb78e (15513486):
> TIFF Directory at offset 0xecb78e (15513486)
>   Subfile Type: reduced-resolution image/multi-page document (3 = 0x3)
1161c1189
< File raw2ometiff_0.8.0/single_plane_legacy.ome.tiff:
---
> File raw2ometiff_0.9.0-SNAPSHOT/single_plane_legacy.ome.tiff:
1163a1192
>   Subfile Type: (0 = 0x0)
1173c1202
<   ImageDescription: <?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:a286ef99-443a-445f-a7dc-4a9340b8acbe" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="test"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="1" SizeT="1" SizeX="5000" SizeY="5000" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData IFD="0" PlaneCount="1"><UUID FileName="single_plane_legacy.ome.tiff">urn:uuid:a286ef99-443a-445f-a7dc-4a9340b8acbe</UUID></TiffData></Pixels></Image><Image ID="Image:1"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:1" SizeC="1" SizeT="1" SizeX="2500" SizeY="2500" SizeZ="1" Type="uint8"><Channel ID="Channel:1:0" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:2"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:2" SizeC="1" SizeT="1" SizeX="1250" SizeY="1250" SizeZ="1" Type="uint8"><Channel ID="Channel:2:0" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:3"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:3" SizeC="1" SizeT="1" SizeX="625" SizeY="625" SizeZ="1" Type="uint8"><Channel ID="Channel:3:0" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:4"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:4" SizeC="1" SizeT="1" SizeX="312" SizeY="312" SizeZ="1" Type="uint8"><Channel ID="Channel:4:0" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:5"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:5" SizeC="1" SizeT="1" SizeX="156" SizeY="156" SizeZ="1" Type="uint8"><Channel ID="Channel:5:0" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image></OME>
---
>   ImageDescription: <?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:fe2f8efe-7676-451c-85ae-21608d5661f4" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="test"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="1" SizeT="1" SizeX="5000" SizeY="5000" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData IFD="0" PlaneCount="1"><UUID FileName="single_plane_legacy.ome.tiff">urn:uuid:fe2f8efe-7676-451c-85ae-21608d5661f4</UUID></TiffData></Pixels></Image><Image ID="Image:1"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:1" SizeC="1" SizeT="1" SizeX="2500" SizeY="2500" SizeZ="1" Type="uint8"><Channel ID="Channel:1:0" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:2"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:2" SizeC="1" SizeT="1" SizeX="1250" SizeY="1250" SizeZ="1" Type="uint8"><Channel ID="Channel:2:0" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:3"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:3" SizeC="1" SizeT="1" SizeX="625" SizeY="625" SizeZ="1" Type="uint8"><Channel ID="Channel:3:0" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:4"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:4" SizeC="1" SizeT="1" SizeX="312" SizeY="312" SizeZ="1" Type="uint8"><Channel ID="Channel:4:0" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image><Image ID="Image:5"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:5" SizeC="1" SizeT="1" SizeX="156" SizeY="156" SizeZ="1" Type="uint8"><Channel ID="Channel:5:0" SamplesPerPixel="1"><LightPath/></Channel></Pixels></Image></OME>
1177c1206,1207
< TIFF Directory at offset 0x4eea4d (5171789)
---
> TIFF Directory at offset 0x4eea75 (5171829)
>   Subfile Type: reduced-resolution image (1 = 0x1)
1190c1220,1221
< TIFF Directory at offset 0x4eec3e (5172286)
---
> TIFF Directory at offset 0x4eec8e (5172366)
>   Subfile Type: reduced-resolution image (1 = 0x1)
1203c1234,1235
< TIFF Directory at offset 0x4eeddf (5172703)
---
> TIFF Directory at offset 0x4eee57 (5172823)
>   Subfile Type: reduced-resolution image (1 = 0x1)
1216c1248,1249
< TIFF Directory at offset 0x4eef40 (5173056)
---
> TIFF Directory at offset 0x4eefe0 (5173216)
>   Subfile Type: reduced-resolution image (1 = 0x1)
1229c1262,1263
< TIFF Directory at offset 0x4ef0a1 (5173409)
---
> TIFF Directory at offset 0x4ef169 (5173609)
>   Subfile Type: reduced-resolution image (1 = 0x1)
1241c1275
< File raw2ometiff_0.8.0/single_plane.ome.tiff:
---
> File raw2ometiff_0.9.0-SNAPSHOT/single_plane.ome.tiff:
1243c1277,1278
< TIFF Directory at offset 0x4ee7d8 (5171160)
---
> TIFF Directory at offset 0x4ee83c (5171260)
>   Subfile Type: (0 = 0x0)
1253,1254c1288,1289
<   SubIFD Offsets: 5169062 5169584 5170026 5170404 5170782
<   ImageDescription: <?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:25644c0e-27d4-4cea-a4ca-6900bc9f30cd" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="test"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="1" SizeT="1" SizeX="5000" SizeY="5000" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData IFD="0" PlaneCount="1"><UUID FileName="single_plane.ome.tiff">urn:uuid:25644c0e-27d4-4cea-a4ca-6900bc9f30cd</UUID></TiffData></Pixels></Image><StructuredAnnotations><MapAnnotation ID="Annotation:Resolution:0" Namespace="openmicroscopy.org/PyramidResolution"><Value><M K="1">2500 2500</M><M K="2">1250 1250</M><M K="3">625 625</M><M K="4">312 312</M><M K="5">156 156</M></Value></MapAnnotation></StructuredAnnotations></OME>
---
>   SubIFD Offsets: 5169062 5169604 5170066 5170464 5170862
>   ImageDescription: <?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:47c684cc-b416-4511-a201-1724abe3d3df" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="test"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="1" SizeT="1" SizeX="5000" SizeY="5000" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData IFD="0" PlaneCount="1"><UUID FileName="single_plane.ome.tiff">urn:uuid:47c684cc-b416-4511-a201-1724abe3d3df</UUID></TiffData></Pixels></Image><StructuredAnnotations><MapAnnotation ID="Annotation:Resolution:0" Namespace="openmicroscopy.org/PyramidResolution"><Value><M K="1">2500 2500</M><M K="2">1250 1250</M><M K="3">625 625</M><M K="4">312 312</M><M K="5">156 156</M></Value></MapAnnotation></StructuredAnnotations></OME>
1271c1306
< TIFF Directory at offset 0x4ee1b0 (5169584)
---
> TIFF Directory at offset 0x4ee1c4 (5169604)
1284c1319
< TIFF Directory at offset 0x4ee36a (5170026)
---
> TIFF Directory at offset 0x4ee392 (5170066)
1297c1332
< TIFF Directory at offset 0x4ee4e4 (5170404)
---
> TIFF Directory at offset 0x4ee520 (5170464)
1310c1345
< TIFF Directory at offset 0x4ee65e (5170782)
---
> TIFF Directory at offset 0x4ee6ae (5170862)
1322,1323c1357,1358
< --- SubIFD 0 of chain 1 at offset 0x4ee1b0 (5169584):
< TIFF Directory at offset 0x4ee1b0 (5169584)
---
> --- SubIFD 0 of chain 1 at offset 0x4ee1c4 (5169604):
> TIFF Directory at offset 0x4ee1c4 (5169604)
1335,1336c1370,1371
< --- SubIFD 1 of chain 1 at offset 0x4ee1b0 (5169584):
< TIFF Directory at offset 0x4ee36a (5170026)
---
> --- SubIFD 1 of chain 1 at offset 0x4ee1c4 (5169604):
> TIFF Directory at offset 0x4ee392 (5170066)
1348,1349c1383,1384
< --- SubIFD 2 of chain 1 at offset 0x4ee1b0 (5169584):
< TIFF Directory at offset 0x4ee4e4 (5170404)
---
> --- SubIFD 2 of chain 1 at offset 0x4ee1c4 (5169604):
> TIFF Directory at offset 0x4ee520 (5170464)
1361,1362c1396,1397
< --- SubIFD 3 of chain 1 at offset 0x4ee1b0 (5169584):
< TIFF Directory at offset 0x4ee65e (5170782)
---
> --- SubIFD 3 of chain 1 at offset 0x4ee1c4 (5169604):
> TIFF Directory at offset 0x4ee6ae (5170862)
1374,1375c1409,1410
< --- SubIFD 0 of chain 2 at offset 0x4ee36a (5170026):
< TIFF Directory at offset 0x4ee36a (5170026)
---
> --- SubIFD 0 of chain 2 at offset 0x4ee392 (5170066):
> TIFF Directory at offset 0x4ee392 (5170066)
1387,1388c1422,1423
< --- SubIFD 1 of chain 2 at offset 0x4ee36a (5170026):
< TIFF Directory at offset 0x4ee4e4 (5170404)
---
> --- SubIFD 1 of chain 2 at offset 0x4ee392 (5170066):
> TIFF Directory at offset 0x4ee520 (5170464)
1400,1401c1435,1436
< --- SubIFD 2 of chain 2 at offset 0x4ee36a (5170026):
< TIFF Directory at offset 0x4ee65e (5170782)
---
> --- SubIFD 2 of chain 2 at offset 0x4ee392 (5170066):
> TIFF Directory at offset 0x4ee6ae (5170862)
1413,1414c1448,1449
< --- SubIFD 0 of chain 3 at offset 0x4ee4e4 (5170404):
< TIFF Directory at offset 0x4ee4e4 (5170404)
---
> --- SubIFD 0 of chain 3 at offset 0x4ee520 (5170464):
> TIFF Directory at offset 0x4ee520 (5170464)
1426,1427c1461,1462
< --- SubIFD 1 of chain 3 at offset 0x4ee4e4 (5170404):
< TIFF Directory at offset 0x4ee65e (5170782)
---
> --- SubIFD 1 of chain 3 at offset 0x4ee520 (5170464):
> TIFF Directory at offset 0x4ee6ae (5170862)
1439,1440c1474,1475
< --- SubIFD 0 of chain 4 at offset 0x4ee65e (5170782):
< TIFF Directory at offset 0x4ee65e (5170782)
---
> --- SubIFD 0 of chain 4 at offset 0x4ee6ae (5170862):
> TIFF Directory at offset 0x4ee6ae (5170862)

The proposed changes all make sense to me as per the TIFF specification i.e.:

  • the TIFF tags stored for each IFD are now consistent between legacy and non-legacy mode except for the SubIFD tag which only applies to pyramidal OME-TIFF
  • the NewSubfileType tag as well as the deprecated SubfileType tag are always set to ensure maximum compatibility with downstream tools
  • the NewSubfileType tag value is making use of the first two bits as defined in the TIFF specification to differentiate full resolution vs reduced resolution as well as single page vs multi-page image

For the legacy mode, I have no further comments to the advanced functional testing performed by @mabruce #145 (review).

For the non-legacy mode, I think there is a case for performing a round of additional validations and some spec clarifications:

  1. we should ensure that the OME-TIFF files written by this version of raw2ometiff are compatible with our tools and notably the Bio-Formats reader. At minimum, that means these files can be reconverted via bioformats2raw and imported into OMERO. Is there any additional tool that should be considered?
  2. the OME-TIFF specification currently recommends to set the NewSubfileType exactly to 1. From the original design document for extending OME-TIFF to support multi-resolutions, The TIFF extension tag SubIFDs must be used to specify sub-resolution image directories. The reduced image bit of the Baseline tag NewSubfileType must be used to distinguish full-resolution images from reduced-size images; the page bit may optionally be set when appropriate, the minimum requirement was to set the reduced image bit which is consistent with the recommendation of the specification. That being said, it would be useful to relax this strict language and update it to tolerate the different values for the NewSubFileType tag of sub-resolutions. I would propose to convert the latter into an ome-model-documentation issue with a proposal that we can discuss with the wider OME team at an upcoming weekly Formats meeting.

@mabruce
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mabruce commented Oct 23, 2025 •
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  1. we should ensure that the OME-TIFF files written by this version of raw2ometiff are compatible with our tools and notably the Bio-Formats reader. At minimum, that means these files can be reconverted via bioformats2raw and imported into OMERO. Is there any additional tool that should be considered?

I've rerun the raw2ometiff command without the --legacy flag to produce an OME-TIFF. This file imports into OMERO with equivalent metadata shown in OMERO.web and can be viewed in PathViewer. It also can be reconverted with bioformats2raw without error.

The OME-TIFF is still not directly openable by OpenSlide as tested with openslide-python, but the reported error is the same with or without this PR's added tags:

>>> s = openslide.OpenSlide('file.ome.tiff')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/path/to/openslide.venv/lib/python3.10/site-packages/openslide/__init__.py", line 207, in __init__
    self._osr = lowlevel.open(filename)
  File "/path/to/openslide.venv/lib/python3.10/site-packages/openslide/lowlevel.py", line 257, in _check_open
    raise OpenSlideUnsupportedFormatError("Unsupported or missing image file")
openslide.lowlevel.OpenSlideUnsupportedFormatError: Unsupported or missing image file

@sbesson sbesson mentioned this pull request Oct 23, 2025
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sbesson approved these changes Nov 19, 2025
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Apologies for the delay here, I have been working on the second point in #145 (review) primarily to ensure files generated with the version of this conversion utility do not deviate from the OME-TIFF specification.

Having raised the issue both at the weekly OME Formats and team meeting, the internal consensus is that it is reasonable to clarify the language in the OME-TIFF specification to be consistent with the changes proposed in this PR i.e. the bit 0 of the NewSubFiletype tag for a pyramidal level IFD should be set to 1 while the bit 1 may be 0 or 1 depending on the scenario.

ome/ome-model-documentation#7 has been opened upstream to propose the specification update and will be shared in image.sc for wider comments. Given the absence of objections so far and the fact this tag is a recommendation in the specification rather than an enforcement, I think the risk associated with merging this and making a release of raw2ometiff is low while it should improves the compatibility of legacy TIFF pyramids or OME-TIFF with other tools in the ecosystem.

@sbesson sbesson merged commit 0beb7cf into glencoesoftware:master Nov 19, 2025
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