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Published 20 hours ago • verified publisher icon computationalpathologygroup

open tif get extra black background

Open zhusihan-python opened this issue 2 years ago • 0 comments

hello, i got some scanned microscopy images and save them in libvips tiffsave as a tif file, when i open it in asap 2.1.0 on windows 11, it shows the tif file in a bigger black background image but it is normal in NDPViewer image the problem is NDPViewer can not recognize the pixel/μm infos, but asap can show the right scale bar and measurement ruler

my tiff infos by tifftools dump

-- .\20230516_2.tif --
Header: 0x4949 <little-endian> <BigTIFF>
Directory 0: offset 270816798 (0x1024561e)
  ImageWidth 256 (0x100) SHORT: 42888
  ImageLength 257 (0x101) SHORT: 45972
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 6 (YCbCr 6 (0x6))
  Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
  SamplesPerPixel 277 (0x115) SHORT: 3
  XResolution 282 (0x11A) RATIONAL: 337500 1 (337500)
  YResolution 283 (0x11B) RATIONAL: 337500 1 (337500)
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  ResolutionUnit 296 (0x128) SHORT: 3 (Centimeter 3 (0x3))
  TileWidth 322 (0x142) SHORT: 1024
  TileLength 323 (0x143) SHORT: 1024
  TileOffsets 324 (0x144) LONG8: <1890> 16 123278 252883 379634 511085 642627 768211 886994 1003702 1132644 1186636 1224814 1299610 1417538 1525938 1613797 1736408 1858482 1976144 2101576 ...
  TileByteCounts 325 (0x145) LONG: <1890> 123262 129605 126751 131451 131542 125584 118783 116708 128942 53992 38178 74796 117928 108400 87859 122611 122074 117662 125432 127684 ...
  SampleFormat 339 (0x153) SHORT: <3> 1 (uint 1 (0x1)) 1 (uint 1 (0x1)) 1 (uint 1 (0x1))
  JPEGTables 347 (0x15B) UNDEFINED: <574> b'\xff\xd8\xff\xdb\x00C\x00\x05\x03\x04\x04\x04\x03\x05\x04\x04\x04\x05\x05\x05' ... (estimated quality: 85)
  ReferenceBlackWhite 532 (0x214) RATIONAL: <6> 0 1 (0) 255 1 (255) 128 1 (128) 255 1 (255) 128 1 (128) 255 1 (255)
Directory 1: offset 366117716 (0x15d28354)
  NewSubfileType 254 (0xFE) LONG: 1 (ReducedImage 1 (0x1))
  ImageWidth 256 (0x100) SHORT: 21444
  ImageLength 257 (0x101) SHORT: 22986
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 6 (YCbCr 6 (0x6))
  Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
  SamplesPerPixel 277 (0x115) SHORT: 3
  XResolution 282 (0x11A) RATIONAL: 337500 1 (337500)
  YResolution 283 (0x11B) RATIONAL: 337500 1 (337500)
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  ResolutionUnit 296 (0x128) SHORT: 3 (Centimeter 3 (0x3))
  TileWidth 322 (0x142) SHORT: 1024
  TileLength 323 (0x143) SHORT: 1024
  TileOffsets 324 (0x144) LONG8: <483> 270840476 271028235 271221492 271417777 271595590 271732378 271797379 271944487 272108420 272275662 272445495 272526818 272679379 272847952 273006863 273136314 273302031 273455216 273604420 273743144 ...
  TileByteCounts 325 (0x145) LONG: <483> 187759 193257 196285 177813 136788 65001 147108 163933 167242 169833 81323 152561 168573 158911 129451 165717 153185 149204 138724 134046 ...
  JPEGTables 347 (0x15B) UNDEFINED: <574> b'\xff\xd8\xff\xdb\x00C\x00\x05\x03\x04\x04\x04\x03\x05\x04\x04\x04\x05\x05\x05' ... (estimated quality: 85)
  ReferenceBlackWhite 532 (0x214) RATIONAL: <6> 0 1 (0) 255 1 (255) 128 1 (128) 255 1 (255) 128 1 (128) 255 1 (255)
Directory 2: offset 400664114 (0x17e1a632)
  NewSubfileType 254 (0xFE) LONG: 1 (ReducedImage 1 (0x1))
  ImageWidth 256 (0x100) SHORT: 10722
  ImageLength 257 (0x101) SHORT: 11493
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 6 (YCbCr 6 (0x6))
  Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
  SamplesPerPixel 277 (0x115) SHORT: 3
  XResolution 282 (0x11A) RATIONAL: 337500 1 (337500)
  YResolution 283 (0x11B) RATIONAL: 337500 1 (337500)
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  ResolutionUnit 296 (0x128) SHORT: 3 (Centimeter 3 (0x3))
  TileWidth 322 (0x142) SHORT: 1024
  TileLength 323 (0x143) SHORT: 1024
  TileOffsets 324 (0x144) LONG8: <132> 366124510 366420538 366702236 366874312 367119602 367356712 367568288 367803238 368026262 368249632 368451064 368564804 368921503 369237721 369440213 369641893 369865931 370147556 370410464 370671543 ...
  TileByteCounts 325 (0x145) LONG: <132> 296028 281698 172076 245290 237110 211576 234950 223024 223370 201432 113740 356699 316218 202492 201680 224038 281625 262908 261079 235573 ...
  JPEGTables 347 (0x15B) UNDEFINED: <574> b'\xff\xd8\xff\xdb\x00C\x00\x05\x03\x04\x04\x04\x03\x05\x04\x04\x04\x05\x05\x05' ... (estimated quality: 85)
  ReferenceBlackWhite 532 (0x214) RATIONAL: <6> 0 1 (0) 255 1 (255) 128 1 (128) 255 1 (255) 128 1 (128) 255 1 (255)
Directory 3: offset 412428652 (0x1895296c)
  NewSubfileType 254 (0xFE) LONG: 1 (ReducedImage 1 (0x1))
  ImageWidth 256 (0x100) SHORT: 5361
  ImageLength 257 (0x101) SHORT: 5746
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 6 (YCbCr 6 (0x6))
  Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
  SamplesPerPixel 277 (0x115) SHORT: 3
  XResolution 282 (0x11A) RATIONAL: 337500 1 (337500)
  YResolution 283 (0x11B) RATIONAL: 337500 1 (337500)
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  ResolutionUnit 296 (0x128) SHORT: 3 (Centimeter 3 (0x3))
  TileWidth 322 (0x142) SHORT: 1024
  TileLength 323 (0x143) SHORT: 1024
  TileOffsets 324 (0x144) LONG8: <36> 400666696 401101762 401398035 401742257 402095403 402412815 402497936 402924021 403329881 403767178 404157539 404505393 404608497 405015235 405447530 405914755 406360757 406802900 406916807 407255289 ...
  TileByteCounts 325 (0x145) LONG: <36> 435066 296273 344222 353146 317412 85121 426085 405860 437297 390361 347854 103104 406738 432295 467225 446002 442143 113907 338482 348078 ...
  JPEGTables 347 (0x15B) UNDEFINED: <574> b'\xff\xd8\xff\xdb\x00C\x00\x05\x03\x04\x04\x04\x03\x05\x04\x04\x04\x05\x05\x05' ... (estimated quality: 85)
  ReferenceBlackWhite 532 (0x214) RATIONAL: <6> 0 1 (0) 255 1 (255) 128 1 (128) 255 1 (255) 128 1 (128) 255 1 (255)
Directory 4: offset 415928470 (0x18ca9096)
  NewSubfileType 254 (0xFE) LONG: 1 (ReducedImage 1 (0x1))
  ImageWidth 256 (0x100) SHORT: 2680
  ImageLength 257 (0x101) SHORT: 2873
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 6 (YCbCr 6 (0x6))
  Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
  SamplesPerPixel 277 (0x115) SHORT: 3
  XResolution 282 (0x11A) RATIONAL: 337500 1 (337500)
  YResolution 283 (0x11B) RATIONAL: 337500 1 (337500)
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  ResolutionUnit 296 (0x128) SHORT: 3 (Centimeter 3 (0x3))
  TileWidth 322 (0x142) SHORT: 1024
  TileLength 323 (0x143) SHORT: 1024
  TileOffsets 324 (0x144) LONG8: <9> 412430082 412897781 413393058 413682590 414108044 414621750 414961984 415313700 415683499
  TileByteCounts 325 (0x145) LONG: <9> 467699 495277 289532 425454 513706 340234 351716 369799 244971
  JPEGTables 347 (0x15B) UNDEFINED: <574> b'\xff\xd8\xff\xdb\x00C\x00\x05\x03\x04\x04\x04\x03\x05\x04\x04\x04\x05\x05\x05' ... (estimated quality: 85)
  ReferenceBlackWhite 532 (0x214) RATIONAL: <6> 0 1 (0) 255 1 (255) 128 1 (128) 255 1 (255) 128 1 (128) 255 1 (255)
Directory 5: offset 416897092 (0x18d95844)
  NewSubfileType 254 (0xFE) LONG: 1 (ReducedImage 1 (0x1))
  ImageWidth 256 (0x100) SHORT: 1340
  ImageLength 257 (0x101) SHORT: 1436
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 6 (YCbCr 6 (0x6))
  Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
  SamplesPerPixel 277 (0x115) SHORT: 3
  XResolution 282 (0x11A) RATIONAL: 337500 1 (337500)
  YResolution 283 (0x11B) RATIONAL: 337500 1 (337500)
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  ResolutionUnit 296 (0x128) SHORT: 3 (Centimeter 3 (0x3))
  TileWidth 322 (0x142) SHORT: 1024
  TileLength 323 (0x143) SHORT: 1024
  TileOffsets 324 (0x144) LONG8: <4> 415929576 416434081 416608193 416815567
  TileByteCounts 325 (0x145) LONG: <4> 504505 174112 207374 81524
  JPEGTables 347 (0x15B) UNDEFINED: <574> b'\xff\xd8\xff\xdb\x00C\x00\x05\x03\x04\x04\x04\x03\x05\x04\x04\x04\x05\x05\x05' ... (estimated quality: 85)
  ReferenceBlackWhite 532 (0x214) RATIONAL: <6> 0 1 (0) 255 1 (255) 128 1 (128) 255 1 (255) 128 1 (128) 255 1 (255)
Directory 6: offset 417140332 (0x18dd0e6c)
  NewSubfileType 254 (0xFE) LONG: 1 (ReducedImage 1 (0x1))
  ImageWidth 256 (0x100) SHORT: 670
  ImageLength 257 (0x101) SHORT: 718
  BitsPerSample 258 (0x102) SHORT: <3> 8 8 8
  Compression 259 (0x103) SHORT: 7 (JPEG 7 (0x7))
  Photometric 262 (0x106) SHORT: 6 (YCbCr 6 (0x6))
  Orientation 274 (0x112) SHORT: 1 (TopLeft 1 (0x1))
  SamplesPerPixel 277 (0x115) SHORT: 3
  XResolution 282 (0x11A) RATIONAL: 337500 1 (337500)
  YResolution 283 (0x11B) RATIONAL: 337500 1 (337500)
  PlanarConfig 284 (0x11C) SHORT: 1 (Chunky 1 (0x1))
  ResolutionUnit 296 (0x128) SHORT: 3 (Centimeter 3 (0x3))
  TileWidth 322 (0x142) SHORT: 1024
  TileLength 323 (0x143) SHORT: 1024
  TileOffsets 324 (0x144) LONG8: 416898138
  TileByteCounts 325 (0x145) LONG8: 242193
  JPEGTables 347 (0x15B) UNDEFINED: <574> b'\xff\xd8\xff\xdb\x00C\x00\x05\x03\x04\x04\x04\x03\x05\x04\x04\x04\x05\x05\x05' ... (estimated quality: 85)
  ReferenceBlackWhite 532 (0x214) RATIONAL: <6> 0 1 (0) 255 1 (255) 128 1 (128) 255 1 (255) 128 1 (128) 255 1 (255)

zhusihan-python avatar May 16 '23 03:05 zhusihan-python