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2010.06.24 19:26 "[Tiff] Anyone work with ScanScope images? (extension is SVS)", by
2010.06.24 19:49 "Re: [Tiff] Anyone work with ScanScope images? (extension is SVS)", by Adam Goode
2010.06.24 22:01 "Re: [Tiff] Anyone work with ScanScope images? (extension is SVS)", by

2010.06.24 19:26 "[Tiff] Anyone work with ScanScope images? (extension is SVS)", by

Hi,

I am working with people from our school's pathology department and they scan images using ScanScope scanner and the images are usually BigTIFF formats.

From the dump info below you can see that there are totally 7 directories.

First one is the full resolution image, second is a thumbnail, Dir #2,#3,#4 are reduced resolution images followed by two more images.

Dir #0, #2, #3 and #4 are using Compression (33003) which is not recognizable by LibTiff. So using tiffcp can only extract other images that use JPG or LZW compression schemes.

Anyone know 33003 compression codec?

I read from ScanScope's documentations that they use JPG, JPG2000 and LZW for compression, but JPG2000 is not 33003.

Any ideas?

Here is an dump info from one image:

//////////////////////////////////////////////////////////////////////////////////////

/home/ginger/Projects/image/sample-HE.svs:
Magic: 0x4949 <little-endian> Version: 0x2a <ClassicTIFF>
Directory 0: offset 896343994 (0x356d1fba) next 897633156 (0x3580cb84)
SubFileType (254) LONG (4) 1<0>
ImageWidth (256) LONG (4) 1<104640>
ImageLength (257) LONG (4) 1<74257>
BitsPerSample (258) SHORT (3) 3<8 8 8>
Compression (259) SHORT (3) 1<33003>
Photometric (262) SHORT (3) 1<2>
ImageDescription (270) ASCII (2) 569<Aperio Image Library v10 ...>
SamplesPerPixel (277) SHORT (3) 1<3>
PlanarConfig (284) SHORT (3) 1<1>
TileWidth (322) SHORT (3) 1<256>
TileLength (323) SHORT (3) 1<256>
TileOffsets (324) LONG (4) 119019<16 178343 357181 532567 708546 894708
1083396 1269947 1460441 1659999 1858478 2050543 2256056 2560524 2914611
3312692 3752329 4223049 4728683 5260082 5812577 6385851 6984002 7600287 ...>
TileByteCounts (325) LONG (4) 119019<480 430 407 480 438 398 523 485 435 417
477 451 454 709 607 499 536 458 653 968 528 452 475 425 ...>
ImageDepth (Silicon Graphics) (32997) LONG (4) 1<1>

ICC Profile (34675) UNDEFINED (7) 141992<00 0x2 0x2a 0xa8 0x41 0x50 0x50 0x4c 0x2 0x40 00 00 0x73 0x63 0x6e 0x72 0x52 0x47 0x42 0x20 0x4c 0x61 0x62 0x20 ...>

Directory 1: offset 897633156 (0x3580cb84) next 1010140174 (0x3c35840e)
SubFileType (254) LONG (4) 1<0>
ImageWidth (256) SHORT (3) 1<1024>
ImageLength (257) SHORT (3) 1<726>
BitsPerSample (258) SHORT (3) 3<8 8 8>
Compression (259) SHORT (3) 1<7>
Photometric (262) SHORT (3) 1<2>
ImageDescription (270) ASCII (2) 537<Aperio Image Library v10 ...>
StripOffsets (273) LONG (4) 46<897438900 897441110 897443692 897446714
897449753 897453282 897456972 897460819 897464625 897468678 897472513
897476310 897479951 897483444 897487045 897490260 897493292 897496293
897500078 897504556 897509293 897514411 897519332 897524276 ...>
SamplesPerPixel (277) SHORT (3) 1<3>
RowsPerStrip (278) SHORT (3) 1<16>
StripByteCounts (279) LONG (4) 46<2210 2582 3022 3039 3529 3690 3847 3806
4053 3835 3797 3641 3493 3601 3215 3032 3001 3785 4478 4737 5118 4921 4944
5415 ...>
PlanarConfig (284) SHORT (3) 1<1>

JPEGTables (347) UNDEFINED (7) 289<0xff 0xd8 0xff 0xdb 00 0x43 00 0xa 0x7 0x7 0x8 0x7 0x6 0xa 0x8 0x8 0x8 0xb 0xa 0xa 0xb 0xe 0x18 0x10 ...>

YCbCrSubsampling (530) SHORT (3) 2<2 2>
ImageDepth (Silicon Graphics) (32997) LONG (4) 1<1>

Directory 2: offset 1010140174 (0x3c35840e) next 1017323116 (0x3ca31e6c)
SubFileType (254) LONG (4) 1<0>
ImageWidth (256) SHORT (3) 1<26160>
ImageLength (257) SHORT (3) 1<18564>
BitsPerSample (258) SHORT (3) 3<8 8 8>
Compression (259) SHORT (3) 1<33003>
Photometric (262) SHORT (3) 1<2>
ImageDescription (270) ASCII (2) 105<Aperio Image Library v10 ...>
SamplesPerPixel (277) SHORT (3) 1<3>
PlanarConfig (284) SHORT (3) 1<1>
TileWidth (322) SHORT (3) 1<256>
TileLength (323) SHORT (3) 1<256>
TileOffsets (324) LONG (4) 7519<897634543 897634948 897635381 897635827
897636251 897636746 897637349 897637824 897638282 897638748 897639258
897639863 897640323 897640780 897641448 897641919 897642511 897642999
897643481 897644200 897646061 897646541 897647030 897647685 ...>
TileByteCounts (325) LONG (4) 7519<405 433 446 424 495 603 475 458 466 510
605 460 457 668 471 592 488 482 719 1861 480 489 655 540 ...>
ImageDepth (Silicon Graphics) (32997) LONG (4) 1<1>

Directory 3: offset 1017323116 (0x3ca31e6c) next 1018782380 (0x3cb962ac)
SubFileType (254) LONG (4) 1<0>
ImageWidth (256) SHORT (3) 1<6540>
ImageLength (257) SHORT (3) 1<4641>
BitsPerSample (258) SHORT (3) 3<8 8 8>
Compression (259) SHORT (3) 1<33003>
Photometric (262) SHORT (3) 1<2>
ImageDescription (270) ASCII (2) 103<Aperio Image Library v10 ...>
SamplesPerPixel (277) SHORT (3) 1<3>
PlanarConfig (284) SHORT (3) 1<1>
TileWidth (322) SHORT (3) 1<256>
TileLength (323) SHORT (3) 1<256>
TileOffsets (324) LONG (4) 494<1010200612 1010201118 1010201855 1010202493
1010203209 1010204015 1010204630 1010205345 1010205894 1010206396 1010206733
1010211273 1010224399 1010231952 1010239555 1010248409 1010262554 1010275753
1010292595 1010308345 1010316179 1010322991 1010324251 1010324725 ...>
TileByteCounts (325) LONG (4) 494<506 737 638 716 806 615 715 549 502 337
4540 13126 7553 7603 8854 14145 13199 16842 15750 7834 6812 1260 474 487
...>
ImageDepth (Silicon Graphics) (32997) LONG (4) 1<1>

Directory 4: offset 1018782380 (0x3cb962ac) next 1019175054 (0x3cbf608e)
SubFileType (254) LONG (4) 1<0>
ImageWidth (256) SHORT (3) 1<3270>
ImageLength (257) SHORT (3) 1<2320>
BitsPerSample (258) SHORT (3) 3<8 8 8>
Compression (259) SHORT (3) 1<33003>
Photometric (262) SHORT (3) 1<2>
ImageDescription (270) ASCII (2) 103<Aperio Image Library v10 ...>
SamplesPerPixel (277) SHORT (3) 1<3>
PlanarConfig (284) SHORT (3) 1<1>
TileWidth (322) SHORT (3) 1<256>
TileLength (323) SHORT (3) 1<256>
TileOffsets (324) LONG (4) 130<1017327352 1017328136 1017328934 1017329632
1017330287 1017330840 1017342164 1017352126 1017367640 1017386104 1017401435
1017405731 1017406541 1017407218 1017408212 1017409281 1017410062 1017410750
1017417783 1017438670 1017456201 1017476880 1017501265 1017524211 ...>
TileByteCounts (325) LONG (4) 130<784 798 698 655 553 11324 9962 15514 18464
15331 4296 810 677 994 1069 781 688 7033 20887 17531 20679 24385 22946 10994
...>
ImageDepth (Silicon Graphics) (32997) LONG (4) 1<1>

Directory 5: offset 1019175054 (0x3cbf608e) next 1019254574 (0x3cc0972e)
SubFileType (254) LONG (4) 1<1>
ImageWidth (256) SHORT (3) 1<412>
ImageLength (257) SHORT (3) 1<396>
BitsPerSample (258) SHORT (3) 3<8 8 8>
Compression (259) SHORT (3) 1<5>
Photometric (262) SHORT (3) 1<2>
ImageDescription (270) ASCII (2) 44<Aperio Image Library v10 ...>
StripOffsets (273) LONG (4) 66<1018783704 1018787775 1018792990 1018798171
1018803419 1018809344 1018815282 1018821144 1018827017 1018832906 1018838841
1018844855 1018850865 1018856947 1018863014 1018869217 1018875316 1018881473
1018887928 1018894530 1018901222 1018907985 1018914649 1018921350 ...>
SamplesPerPixel (277) SHORT (3) 1<3>
RowsPerStrip (278) SHORT (3) 1<6>
StripByteCounts (279) LONG (4) 66<4071 5215 5181 5248 5925 5938 5862 5873
5889 5935 6014 6010 6082 6067 6203 6099 6157 6455 6602 6692 6763 6664 6701
6631 ...>
PlanarConfig (284) SHORT (3) 1<1>
Predictor (317) SHORT (3) 1<2>
ImageDepth (Silicon Graphics) (32997) LONG (4) 1<1>

Directory 6: offset 1019254574 (0x3cc0972e) next 0 (0)
SubFileType (254) LONG (4) 1<9>
ImageWidth (256) SHORT (3) 1<1280>
ImageLength (257) SHORT (3) 1<400>
BitsPerSample (258) SHORT (3) 3<8 8 8>
Compression (259) SHORT (3) 1<7>
Photometric (262) SHORT (3) 1<2>
ImageDescription (270) ASCII (2) 45<Aperio Image Library v10 ...>
StripOffsets (273) LONG (4) 25<1019175806 1019181364 1019184683 1019188356
1019191016 1019193407 1019195875 1019198347 1019200809 1019203128 1019205695
1019208884 1019211889 1019215109 1019218392 1019221621 1019224403 1019227309
1019230343 1019233314 1019236129 1019240023 1019242361 1019244557 ...>
SamplesPerPixel (277) SHORT (3) 1<3>
RowsPerStrip (278) SHORT (3) 1<16>
StripByteCounts (279) LONG (4) 25<5558 3319 3673 2660 2391 2468 2472 2462
2319 2567 3189 3005 3220 3283 3229 2782 2906 3034 2971 2815 3894 2338 2196
3220 ...>
PlanarConfig (284) SHORT (3) 1<1>

JPEGTables (347) UNDEFINED (7) 289<0xff 0xd8 0xff 0xdb 00 0x43 00 0x10 0xb 0xc 0xe 0xc 0xa 0x10 0xe 0xd 0xe 0x12 0x11 0x10 0x13 0x18 0x28 0x1a ...>

YCbCrSubsampling (530) SHORT (3) 2<2 2>
ImageDepth (Silicon Graphics) (32997) LONG (4) 1<1>

//////////////////////////////////////////////////////////////////////////////////////

Ginger Jing Han