Incorrect handling of images with labels

[sbesson]

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