Reading file exported from Aperio ImageScope

[Kent Johnson]

I tried saving as SVS:JPEG. The key issue seems to be whether there are
multiple levels. If I save a small image in SVS:JPEG format, so it has only
one level (plus thumbnail, label and macro images), OpenSlide behaves as I
described before - it ignores the true thumbnail and the label image and
returns the macro image as the thumbnail. If I save a larger image with two
levels, OpenSlide behaves correctly.

Kent


On Tue, Nov 6, 2012 at 12:59 PM, Cornwell, Carl (NIH/NLM/LHC) [C] <
ccornwell at mail.nih.gov> wrote:

> It looks like you selected Output/Compression as TIF:LZW - is that
> correct? If so, can you redo the export with Output/Compression set to
> SVS:JPEG or SVS:JPEG2000?
>
> The OpenSlide code (openslide-vendor-aperios.c) accepts the current file
> as Aperio based only on the appearance of "Aperio" in the image
> description, then applies various checks which initially pass and identify
> the components correctly - so, in theory it should correctly assign the
> sub-images in your file. However, it looks like the LZW compression may be
> causing some problems - note the unrecognized tag 347 - although I can't
> see  exactly why in the code.
>
> Perhaps one of the experts will chime in soon.
>
> --
> Carl Cornwell
> Contractor
> Lister Hill National Center For
>    Biomedical Communications
> National Library of Medicine
> 8600 Rockville Pike
> Bldg. 38A, Room 10S1015D
> Bethesda, MD 20894
> Voice (301) 435-5187
>
> ________________________________
> From: Kent Johnson [kent3737 at gmail.com]
> Sent: Tuesday, November 06, 2012 10:22 AM
> To: openslide-users at lists.andrew.cmu.edu
> Subject: Reading file exported from Aperio ImageScope
>
> Hi,
>
> I'm trying to use OpenSlide (openslide-win32-20120908) to read a
> partial-slide TIFF file exported from Aperio ImageScope. The file is
> recognized as an Aperio file but the component images are not interpreted
> correctly.
>
> The first image is read by OpenSlide as the level 0 image. The second
> image is a thumbnail. The third image is a label image and the fourth is a
> macro image. OpenSlide ignores the second and third images and uses the
> macro image as the thumbnail.
>
> My expectation is that the second image would be used as the thumbnail and
> the label and macro images would be included as associated images. Is this
> something that should work correctly or am I stretching OpenSlide a bit too
> much?
>
> Below is the tiffinfo output for the image.
>
> Thanks,
> Kent
>
> TIFF Directory at offset 0xc7563e
>   Subfile Type: (0 = 0x0)
>   Image Width: 3278 Image Length: 3026 Image Depth: 1
>   Tile Width: 240 Tile Length: 240
>   Bits/Sample: 8
>   Compression Scheme: LZW
>   Photometric Interpretation: RGB color
>   Image Description: "Aperio Image Library v11.2.1 \r\n68340x43430
> [49868,23390 3278x3026] (240x240) LZW;Aperio Image Library v8.0
> .19\n69360x43530 [0,0 68340x43430] (240x240) JPEG/RGB Q=70|AppMag =
> 20|StripeWidth = 2034|ScanScope ID = PHUSCA-W20585|Filename =
> 13203|Title = none|Date = 01/03/07|Time = 14:09:11|User =
> f92fa4e0-e189-4a07-bb9b-095c3f5bbde4|MPP = 0.4667|Left = 9.760571|Top =
> 22.175273|LineCameraSkew = 0.000000|LineAreaXOffset =
> 0.000000|LineAreaYOffset = 0.000000|DSR ID = 192.168.2.102|ImageID = 13203|O
> riginalWidth = 69360|Originalheight = 43530|OriginalWidth =
> 68340|OriginalHeight = 43430"
>   Samples/Pixel: 3
>   Planar Configuration: single image plane
>   Predictor: horizontal differencing 2 (0x2)
> TIFF Directory at offset 0xd93922
>   Subfile Type: (0 = 0x0)
>   Image Width: 831 Image Length: 768 Image Depth: 1
>   Bits/Sample: 8
>   Compression Scheme: LZW
>   Photometric Interpretation: RGB color
>   Image Description: "Aperio Image Library v11.2.1 \n3278x3026 -> 831x768
> - ;Aperio Image Library v8.0.19\n69360x43530 [0,0 68340x
> 43430] (240x240) JPEG/RGB Q=70|AppMag = 20|StripeWidth = 2034|ScanScope ID
> = PHUSCA-W20585|Filename = 13203|Title = none|Date = 01
> /03/07|Time = 14:09:11|User = f92fa4e0-e189-4a07-bb9b-095c3f5bbde4|MPP =
> 0.4667|Left = 9.760571|Top = 22.175273|LineCameraSkew = 0
> .000000|LineAreaXOffset = 0.000000|LineAreaYOffset = 0.000000|DSR ID =
> 192.168.2.102|ImageID = 13203|OriginalWidth = 69360|Origina
> lheight = 43530|OriginalWidth = 68340|OriginalHeight = 43430"
>   Samples/Pixel: 3
>   Rows/Strip: 3
>   Planar Configuration: single image plane
>   Predictor: horizontal differencing 2 (0x2)
> TIFF Directory at offset 0xdb0ede
>   Subfile Type: reduced-resolution image (1 = 0x1)
>   Image Width: 356 Image Length: 320 Image Depth: 1
>   Bits/Sample: 8
>   Compression Scheme: LZW
>   Photometric Interpretation: RGB color
>   Image Description: "Aperio Image Library v11.2.1 \nlabel 356x320"
>   Samples/Pixel: 3
>   Rows/Strip: 7
>   Planar Configuration: single image plane
>   Predictor: horizontal differencing 2 (0x2)
> TIFFReadDirectory: Warning, exported from ImageScope 13203.tif: unknown
> field with tag 347 (0x15b) encountered.
> TIFF Directory at offset 0xdbcd6c
>   Subfile Type: reduced-resolution image (9 = 0x9)
>   Image Width: 640 Image Length: 246 Image Depth: 1
>   Bits/Sample: 8
>   Compression Scheme: JPEG
>   Photometric Interpretation: RGB color
>   YCbCr Subsampling: 2, 2
>   Image Description: "Aperio Image Library v11.2.1 \nmacro 640x246"
>   Samples/Pixel: 3
>   Rows/Strip: 16
>   Planar Configuration: single image plane
>   Tag 347: <unsupported data type in TIFFPrint>
>
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