Hi,
I have downloaded some trestle .tif and .scn images from here (http://openslide.cs.cmu.edu/download/openslide-testdata/Trestle/).
When I load this image with an openslide I can see the series of pyramid structure as below:
levels dimensions: ((40000, 27712), (20000, 13856), (10000, 6928), (4992, 3456), (2496, 1728), (1248, 864), (624, 432))
But when load the same image with python-bioformats then it just shows or select first series 0 = (40000, 27712), not all.
I pass below code to do that:
# setup reader
reader = bioformats.ImageReader(input_any1)
omeMeta = bioformats.metadatatools.createOMEXMLMetadata()
reader.setMetadataStore(omeMeta)
reader.setId(input_any1)
metadata = javabridge.jdictionary_to_string_dictionary(reader.rdr.getMetadata())
get = reader.rdr.getSeriesCount(input_any1)
gett = reader.rdr.getImageCount(input_any1)
The output of get is 1, I believe it should be 7 as below shown by bftools.
**Anyway, I also tried to visualize the metadata of this image using bftools and it shows that image has 7 **
series as provided below:
Reading core metadata
filename = 111.tif
Series count = 7
Series #0 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 40000
Height = 27712
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 21632 x 15360
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #1 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 20000
Height = 13856
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 21632 x 15360
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
Series #2 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 10000
Height = 6928
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 21632 x 15360
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
Series #3 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 4992
Height = 3456
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 21632 x 15360
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
Series #4 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 2496
Height = 1728
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 21632 x 15360
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
Series #5 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 1248
Height = 864
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 21632 x 15360
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
Series #6 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 624
Height = 432
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 21632 x 15360
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
Reading global metadata
Background Color: E6E6E6
BitsPerSample: 8
Compression: JPEG
Copyright: (c) 2005 Trestle Corp.
DateTime: 2010:01:04 14:41:53
HostComputer: TRESTLE-CP01
ImageLength: 33792
ImageWidth: 46592
JPEG Quality: 75
MetaDataPhotometricInterpretation: RGB
NumberOfChannels: 3
Objective Power: 10
Orientation: 1st row - top; 1st column - left
OverlapsXY: 64 64 32 32 16 16
PhotometricInterpretation: YCbCr
PlanarConfiguration: Chunky
ReferenceBlackWhite: 0
SamplesPerPixel: 3
Software: MedScan v3.4.2.1 - Release
TileByteCounts: 2503
TileLength: 352
TileOffsets: 8
TileWidth: 448
White Balance: C0AAA1
XPosition: 44595
XResolution: 0.574691891670227
YCbCrSubSampling: chroma image dimensions are half the luma image dimensions
YPosition: 23405
YResolution: 0.5750624537467957
And, I have another question too:
When I load SCN image with python-bioformats it shows me that, there are 27 series:
Checking file format [Leica SCN]
Initializing reader
LeicaSCNReader initializing /Users/yubraj/Desktop/urgent_wsi/input/Leica-2.scn
Reading IFDs
Populating metadata
Populating OME metadata
Initialization took 0.248s
Reading core metadata
filename = /Users/yubraj/Desktop/urgent_wsi/input/Leica-2.scn
Series count = 27
Series #0 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 1616
Height = 4668
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 44 x 128
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #1 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 404
Height = 1167
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 44 x 128
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #2 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 101
Height = 291
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 44 x 128
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
Series #3 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 39168
Height = 26048
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #4 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 9792
Height = 6512
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #5 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 2448
Height = 1628
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #6 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 612
Height = 407
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #7 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 153
Height = 101
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #8 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 38
Height = 25
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
Series #9 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 39360
Height = 23360
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #10 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 9840
Height = 5840
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #11 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 2460
Height = 1460
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #12 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 615
Height = 365
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #13 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 154
Height = 91
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #14 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 38
Height = 22
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
Series #15 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 39360
Height = 23360
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #16 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 9840
Height = 5840
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #17 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 2460
Height = 1460
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #18 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 615
Height = 365
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #19 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 154
Height = 91
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #20 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 38
Height = 22
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 22
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
Series #21 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 39168
Height = 26048
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #22 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 9792
Height = 6512
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #23 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 2448
Height = 1628
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #24 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 612
Height = 407
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #25 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 153
Height = 101
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #26 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 38
Height = 25
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Thumbnail size = 38 x 25
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
Reading global metadata
BitsPerSample: 8
Compression: JPEG
ImageLength: 4668
ImageWidth: 1616
MetaDataPhotometricInterpretation: RGB
NumberOfChannels: 3
PhotometricInterpretation: YCbCr
PlanarConfiguration: Chunky
ReferenceBlackWhite: 0
ResolutionUnit: Centimeter
SamplesPerPixel: 3
TileLength: 512
TileWidth: 512
XResolution: 608.3301634770519
YCbCrSubSampling: chroma image dimensions are half the luma image dimensions
YResolution: 608.3301634770519
Reading series #0 metadata
collection.name: ImageCollection_0000002583
collection.uuid: urn:uuid:85036cce-a631-4ea1-9da8-c197977aae03
creationDate: 2014-11-26T14:16:39.753Z
device.model for image: Leica SCN400;Leica SCN
device.version for image: 1.5.1.10804 2012/05/10 13:29:07;1.5.1.10864
scanSettings.illuminationSettings.illuminationSource for image: brightfield
scanSettings.illuminationSettings.numericalAperture for image: 0.65
scanSettings.objectiveSettings.objective for image: 40
view.offsetX for image: 8971682
view.offsetY for image: 40843483
view.sizeX for image: 9792000
view.sizeY for image: 6512000
view.spacingZ for image: 400
But when I load the same image with openslide it just shows 6 series as follows:
level_dimensions: ((106259, 306939), (26565, 76735), (6642, 19184), (1661, 4796), (416, 1201), (104, 298))
What is going on here? I didnât understand the concept of this image.
Can anyone please help me to clarify how to solve this problem?
Images can be downloaded from :
Any suggestion