tiffslide not reading MPP of CAMELYON16 but openslide does

kaczmarj commented 1 year ago

hello, i am using tiffslide with the camelyon16 dataset. i realized that tiffslide cannot read the mpp of these images, whereas openslide-python can. i have included info below on how to reproduce this behavior:

create python environment and download camelyon16 file:

# Create python env
python3.10 -m venv --upgrade-deps venv/
source ./venv/bin/activate
python -m pip install awscli openslide-python tiffslide

# Copy sample file from CAMELYON16
aws s3 cp --no-sign-request s3://camelyon-dataset/CAMELYON16/images/normal_001.tif .

read mpp with openslide and tiffslide:

>>> import openslide, tiffslide
>>> oslide = openslide.open_slide("normal_001.tif")
>>> oslide.properties[openslide.PROPERTY_NAME_MPP_X]
'0.24309399999999998'
>>> tslide = tiffslide.open_slide("normal_001.tif")
>>> tslide.properties[tiffslide.PROPERTY_NAME_MPP_X]
>>> tslide.properties[tiffslide.PROPERTY_NAME_MPP_X] is None
True

here are the openslide-python and tiffslide versions

>>> import openslide, tiffslide
>>> openslide.__version__
'1.3.0'
>>> tiffslide.__version__
'2.2.0'

ap-- commented 1 year ago

Hey @kaczmarj

Thanks for opening the issue! This seems to be a philips tiff file, and we would need to add support in _PropertyParser

There would need to be an entry here: https://github.com/Bayer-Group/tiffslide/blob/8bea5a4c8e1429071ade6d4c40169ce153786d19/tiffslide/tiffslide.py#L642-L648

and a corresponding metadata parsing method like parse_aperio or parse_leica.

Would you want to work on a PR?

Cheers, Andreas :smiley:

kaczmarj commented 1 year ago

thanks @ap-- - i don't have the bandwidth at this time to learn about phillips tiff and create a pr for this issue. but if anyone else reading along feels motivated to address this, i have pasted the output of openslide-show-properties for s3://camelyon-dataset/CAMELYON16/images/normal_001.tif

openslide.level-count: '10'
openslide.level[0].downsample: '1'
openslide.level[0].height: '221184'
openslide.level[0].tile-height: '512'
openslide.level[0].tile-width: '512'
openslide.level[0].width: '97792'
openslide.level[1].downsample: '2'
openslide.level[1].height: '110592'
openslide.level[1].tile-height: '512'
openslide.level[1].tile-width: '512'
openslide.level[1].width: '48896'
openslide.level[2].downsample: '4'
openslide.level[2].height: '55296'
openslide.level[2].tile-height: '512'
openslide.level[2].tile-width: '512'
openslide.level[2].width: '24448'
openslide.level[3].downsample: '8'
openslide.level[3].height: '27648'
openslide.level[3].tile-height: '512'
openslide.level[3].tile-width: '512'
openslide.level[3].width: '12224'
openslide.level[4].downsample: '16'
openslide.level[4].height: '13824'
openslide.level[4].tile-height: '512'
openslide.level[4].tile-width: '512'
openslide.level[4].width: '6112'
openslide.level[5].downsample: '32'
openslide.level[5].height: '6912'
openslide.level[5].tile-height: '512'
openslide.level[5].tile-width: '512'
openslide.level[5].width: '3056'
openslide.level[6].downsample: '64'
openslide.level[6].height: '3456'
openslide.level[6].tile-height: '512'
openslide.level[6].tile-width: '512'
openslide.level[6].width: '1528'
openslide.level[7].downsample: '128'
openslide.level[7].height: '1728'
openslide.level[7].tile-height: '512'
openslide.level[7].tile-width: '512'
openslide.level[7].width: '764'
openslide.level[8].downsample: '256'
openslide.level[8].height: '864'
openslide.level[8].tile-height: '512'
openslide.level[8].tile-width: '512'
openslide.level[8].width: '382'
openslide.level[9].downsample: '512'
openslide.level[9].height: '432'
openslide.level[9].tile-height: '512'
openslide.level[9].tile-width: '512'
openslide.level[9].width: '191'
openslide.mpp-x: '0.24309399999999998'
openslide.mpp-y: '0.24309399999999998'
openslide.quickhash-1: 'cc2b83f3fd7391491124031fcf20459a478e424e5a87b66aefcaee48f39973a2'
openslide.vendor: 'philips'
philips.DICOM_BITS_ALLOCATED: '8'
philips.DICOM_BITS_STORED: '8'
philips.DICOM_DERIVATION_DESCRIPTION: 'tiff-useBigTIFF=1-useRgb=0-levels=10003,10002,10000,10001-processing=0-q80-sourceFilename="T11-07929-I1-6"'
philips.DICOM_HIGH_BIT: '7'
philips.DICOM_LOSSY_IMAGE_COMPRESSION: '01'
philips.DICOM_LOSSY_IMAGE_COMPRESSION_METHOD: '"PHILIPS_TIFF_1_0"'
philips.DICOM_LOSSY_IMAGE_COMPRESSION_RATIO: '"3"'
philips.DICOM_MANUFACTURER: '3D Histech'
philips.DICOM_PHOTOMETRIC_INTERPRETATION: 'RGB'
philips.DICOM_PIXEL_REPRESENTATION: '0'
philips.DICOM_PIXEL_SPACING: '"0.000243094" "0.000243094"'
philips.DICOM_PLANAR_CONFIGURATION: '0'
philips.DICOM_SAMPLES_PER_PIXEL: '3'
philips.DICOM_SOFTWARE_VERSIONS: '"4.0.3"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[0].DICOM_PIXEL_SPACING: '"0.000243902" "0.000243902"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[0].PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION: '"0" "0" "0"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[0].PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS: '97792'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[0].PIIM_PIXEL_DATA_REPRESENTATION_NUMBER: '0'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[0].PIIM_PIXEL_DATA_REPRESENTATION_ROWS: '221184'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[1].DICOM_PIXEL_SPACING: '"0.000487805" "0.000487805"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[1].PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION: '"0" "0" "0"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[1].PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS: '49152'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[1].PIIM_PIXEL_DATA_REPRESENTATION_NUMBER: '1'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[1].PIIM_PIXEL_DATA_REPRESENTATION_ROWS: '110592'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[2].DICOM_PIXEL_SPACING: '"0.00097561" "0.00097561"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[2].PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION: '"0" "0" "0"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[2].PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS: '24576'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[2].PIIM_PIXEL_DATA_REPRESENTATION_NUMBER: '2'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[2].PIIM_PIXEL_DATA_REPRESENTATION_ROWS: '55296'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[3].DICOM_PIXEL_SPACING: '"0.00195122" "0.00195122"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[3].PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION: '"0" "0" "0"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[3].PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS: '12288'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[3].PIIM_PIXEL_DATA_REPRESENTATION_NUMBER: '3'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[3].PIIM_PIXEL_DATA_REPRESENTATION_ROWS: '27648'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[4].DICOM_PIXEL_SPACING: '"0.00390244" "0.00390244"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[4].PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION: '"0" "0" "0"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[4].PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS: '6144'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[4].PIIM_PIXEL_DATA_REPRESENTATION_NUMBER: '4'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[4].PIIM_PIXEL_DATA_REPRESENTATION_ROWS: '13824'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[5].DICOM_PIXEL_SPACING: '"0.00780488" "0.00780488"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[5].PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION: '"0" "0" "0"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[5].PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS: '3072'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[5].PIIM_PIXEL_DATA_REPRESENTATION_NUMBER: '5'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[5].PIIM_PIXEL_DATA_REPRESENTATION_ROWS: '7168'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[6].DICOM_PIXEL_SPACING: '"0.0156098" "0.0156098"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[6].PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION: '"0" "0" "0"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[6].PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS: '1536'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[6].PIIM_PIXEL_DATA_REPRESENTATION_NUMBER: '6'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[6].PIIM_PIXEL_DATA_REPRESENTATION_ROWS: '3584'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[7].DICOM_PIXEL_SPACING: '"0.0312195" "0.0312195"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[7].PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION: '"0" "0" "0"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[7].PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS: '1024'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[7].PIIM_PIXEL_DATA_REPRESENTATION_NUMBER: '7'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[7].PIIM_PIXEL_DATA_REPRESENTATION_ROWS: '2048'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[8].DICOM_PIXEL_SPACING: '"0.062439" "0.062439"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[8].PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION: '"0" "0" "0"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[8].PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS: '512'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[8].PIIM_PIXEL_DATA_REPRESENTATION_NUMBER: '8'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[8].PIIM_PIXEL_DATA_REPRESENTATION_ROWS: '1024'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[9].DICOM_PIXEL_SPACING: '"0.124878" "0.124878"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[9].PIIM_DP_PIXEL_DATA_REPRESENTATION_POSITION: '"0" "0" "0"'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[9].PIIM_PIXEL_DATA_REPRESENTATION_COLUMNS: '512'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[9].PIIM_PIXEL_DATA_REPRESENTATION_NUMBER: '9'
philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[9].PIIM_PIXEL_DATA_REPRESENTATION_ROWS: '512'
philips.PIM_DP_IMAGE_COLUMNS: '97792'
philips.PIM_DP_IMAGE_ROWS: '221184'
philips.PIM_DP_IMAGE_TYPE: 'WSI'
philips.PIM_DP_SOURCE_FILE: '%FILENAME%'
philips.PIM_DP_UFS_INTERFACE_VERSION: '3.0'
philips.UFS_IMAGE_PIXEL_TRANSFORMATION_METHOD: '0'
tiff.ResolutionUnit: 'inch'
tiff.Software: 'Philips DP v1.0'

the mpp appears to come from

philips.DICOM_PIXEL_SPACING: '"0.000243094" "0.000243094"'

because those values agree with openslide.mpp-x and openslide.mpp-y, but there is also a level 0 pixel spacing entry, which is slightly different.

philips.PIIM_PIXEL_DATA_REPRESENTATION_SEQUENCE[0].DICOM_PIXEL_SPACING: '"0.000243902" "0.000243902"'

openslide's website says the following (source):

openslide.mpp-x
    calculated as 1000 * philips.DICOM_PIXEL_SPACING[1]
openslide.mpp-y
    calculated as 1000 * philips.DICOM_PIXEL_SPACING[0]

ap-- commented 1 year ago

i don't have the bandwidth at this time to learn about phillips tiff and create a pr

No worries 😊 and thanks for providing the additional information. All of this can be parsed out of the XML stored image description of the file.

If anyone is up for it, this is a nice and self contained issue to work on:

Add an entry to the dict in _PropertyParser mentioned above. (This will dispatch to a method named parse_philips())
In parse_phillips() get the image description tag content, parse the XML and extract the values from the comment above.

Happy to answer further questions, and provide guidance with the PR.

Cheers, Andreas 😊

Bayer-Group / tiffslide

tiffslide not reading MPP of CAMELYON16 but openslide does #77