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Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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VSI: not recognizing image pyramid #4015

Open jboulanger opened 1 year ago

jboulanger commented 1 year ago

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,

dgault commented 1 year ago

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.

dgault commented 2 months ago

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
imagesc-bot commented 2 months ago

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