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VSI: not recognizing image pyramid
Hello, I have a VSI file exported from the Evident software which is made of a single vsi file (with no ets pyramid) as it is only a few kB or MB. In that case, bioformats does not seem to decode properly the image serie but only the macro image. Here is a picture https://cloud.mrc-lmb.cam.ac.uk/s/PT5FeBsxkMkabxy I hope this helps. All the best,
Thanks @jboulanger, with the latest Bio-Formats it seems to have picked up 2 series, both labeled as macro image, the first 152 x 167 (3 channels) and the second 62 x 68 (5 channels). The second does not display correctly and is scrambled.
A similar issue has been reported in forum thread https://forum.image.sc/t/open-vsi-ome-tiff-files-with-tif-pixel-data/96327/9
A sample dataset acquired from Olympus VS200 has been provided and reproduces the issue with Bio-Formats 7.3.0. The samples files are at https://drive.google.com/drive/folders/10PX3ivPcWImZJF2DYKsiztp0cHM_ZZIu and I will copy them over to inbox for testing
In the dataset, it includes a .tiff file which appears to have multiple resolutions and has no associated .ets file.
When opening the .vsi file (in this case fluorescent.vsi from the sample data), we have 3 series as below, the last of which seems to be the lowest level resolution:
Series count = 3
Series #0 :
Image count = 1
RGB = true (3)
Interleaved = false
Indexed = false (true color)
Width = 991
Height = 375
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Tile size = 991 x 375
Thumbnail size = 128 x 48
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 = 495
Height = 284
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Tile size = 495 x 64
Thumbnail size = 128 x 73
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 = false (1)
Interleaved = false
Indexed = false (true color)
Width = 454
Height = 374
SizeZ = 1
SizeT = 1
SizeC = 1
Tile size = 454 x 64
Thumbnail size = 128 x 105
Endianness = intel (little)
Dimension order = XYCZT (uncertain)
Pixel type = uint16
Valid bits per pixel = 16
Metadata complete = true
Thumbnail series = true
-----
Plane #0 <=> Z 0, C 0, T 0
When opening the tiff file on its own (frame_t_0-001.tiff from the sample data) it is read as an OME-TIFF file, but even with the noflat option each of the resolutions appears as a seperate series:
Series count = 7
Reading IFDs
Populating metadata
Series #0 :
Image count = 3
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 29074
Height = 23985
SizeZ = 1
SizeT = 1
SizeC = 3
Tile size = 512 x 512
Thumbnail size = 128 x 105
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint16
Valid bits per pixel = 16
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Plane #1 <=> Z 0, C 1, T 0
Plane #2 <=> Z 0, C 2, T 0
Series #1 :
Image count = 3
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 14537
Height = 11992
SizeZ = 1
SizeT = 1
SizeC = 3
Tile size = 512 x 512
Thumbnail size = 128 x 105
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint16
Valid bits per pixel = 16
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Plane #1 <=> Z 0, C 1, T 0
Plane #2 <=> Z 0, C 2, T 0
Series #2 :
Image count = 3
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 7268
Height = 5996
SizeZ = 1
SizeT = 1
SizeC = 3
Tile size = 512 x 512
Thumbnail size = 128 x 105
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint16
Valid bits per pixel = 16
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Plane #1 <=> Z 0, C 1, T 0
Plane #2 <=> Z 0, C 2, T 0
Series #3 :
Image count = 3
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 3634
Height = 2998
SizeZ = 1
SizeT = 1
SizeC = 3
Tile size = 512 x 512
Thumbnail size = 128 x 105
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint16
Valid bits per pixel = 16
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Plane #1 <=> Z 0, C 1, T 0
Plane #2 <=> Z 0, C 2, T 0
Series #4 :
Image count = 3
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 1817
Height = 1499
SizeZ = 1
SizeT = 1
SizeC = 3
Tile size = 512 x 512
Thumbnail size = 128 x 105
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint16
Valid bits per pixel = 16
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Plane #1 <=> Z 0, C 1, T 0
Plane #2 <=> Z 0, C 2, T 0
Series #5 :
Image count = 3
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 908
Height = 749
SizeZ = 1
SizeT = 1
SizeC = 3
Tile size = 512 x 512
Thumbnail size = 128 x 105
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint16
Valid bits per pixel = 16
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Plane #1 <=> Z 0, C 1, T 0
Plane #2 <=> Z 0, C 2, T 0
Series #6 :
Image count = 3
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 454
Height = 374
SizeZ = 1
SizeT = 1
SizeC = 3
Tile size = 454 x 374
Thumbnail size = 128 x 105
Endianness = intel (little)
Dimension order = XYCZT (certain)
Pixel type = uint16
Valid bits per pixel = 16
Metadata complete = true
Thumbnail series = false
-----
Plane #0 <=> Z 0, C 0, T 0
Plane #1 <=> Z 0, C 1, T 0
Plane #2 <=> Z 0, C 2, T 0
This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/open-vsi-ome-tiff-files-with-tif-pixel-data/96327/12
