Taking the examples of ome-ngff/0.3/idr/idr0095B/11511419.zarr
(java_dev) sbesson@Sebastiens-MacBook-Pro bftools % BF_CP=~/Downloads/OMEZarrReader-0.1.0-SNAPSHOT.jar ./showinf ~/Desktop/idr0095B/11511419.zarr/.zattrs -noflat -nopix
...
Series count = 7
Series #0 :
Resolutions = 7
sizeX[0] = 2048
sizeX[1] = 1024
sizeX[2] = 512
sizeX[3] = 256
sizeX[4] = 128
sizeX[5] = 64
sizeX[6] = 2048
Image count = 3
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 2048
Height = 2048
SizeZ = 3
SizeT = 1
SizeC = 1
Tile size = 1 x 2048
Thumbnail size = 128 x 128
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = uint16
Valid bits per pixel = 16
Metadata complete = false
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Plane #1 <=> Z 1, C 0, T 0
Plane #2 <=> Z 2, C 0, T 0
Series #1 :
Image count = 1
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 1024
Height = 1024
SizeZ = 1
SizeT = 1
SizeC = 1
Tile size = 1 x 256
Thumbnail size = 128 x 128
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = double
Valid bits per pixel = 64
Metadata complete = false
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #2 :
Image count = 1
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 512
Height = 512
SizeZ = 1
SizeT = 1
SizeC = 1
Tile size = 1 x 128
Thumbnail size = 128 x 128
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = double
Valid bits per pixel = 64
Metadata complete = false
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #3 :
Image count = 1
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 256
Height = 256
SizeZ = 1
SizeT = 1
SizeC = 1
Tile size = 1 x 128
Thumbnail size = 128 x 128
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = double
Valid bits per pixel = 64
Metadata complete = false
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #4 :
Image count = 1
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 128
Height = 128
SizeZ = 1
SizeT = 1
SizeC = 1
Tile size = 1 x 128
Thumbnail size = 128 x 128
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = double
Valid bits per pixel = 64
Metadata complete = false
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #5 :
Image count = 1
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 64
Height = 64
SizeZ = 1
SizeT = 1
SizeC = 1
Tile size = 1 x 64
Thumbnail size = 64 x 64
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = double
Valid bits per pixel = 64
Metadata complete = false
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Series #6 :
Image count = 1
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 32
Height = 32
SizeZ = 1
SizeT = 1
SizeC = 1
Tile size = 1 x 32
Thumbnail size = 32 x 32
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = double
Valid bits per pixel = 64
Metadata complete = false
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Reading global metadata
Axis:0:0: c
Axis:0:1: y
Axis:0:2: x
Reading series #0 metadata
The first resolution of the label image is appended to the image resolutions and each follow-up label resolution is detected as a separate image of pixel type double.
Since labels are not really supported by the OME ROI model, I see two options to handle these datasets up for discussion:
discard any label image
treat label images as additional multi-resolution series
Taking the examples of
ome-ngff/0.3/idr/idr0095B/11511419.zarrThe first resolution of the label image is appended to the image resolutions and each follow-up label resolution is detected as a separate image of pixel type
double.Since labels are not really supported by the OME ROI model, I see two options to handle these datasets up for discussion: