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Image is being incorrectly interpreted as 16bit instead of 8bit #72

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tlnagy opened this issue Feb 17, 2022 · 5 comments
Open

Image is being incorrectly interpreted as 16bit instead of 8bit #72

tlnagy opened this issue Feb 17, 2022 · 5 comments
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bug Something isn't working

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@tlnagy
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tlnagy commented Feb 17, 2022 •
edited
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Does this mean you get an all-zero channel after loading it even before visualization?

Exactly. Apart from that it seems to be taking the pixel values in each slice (z) from different channels randomly, meaning that in slice 21 I'd be getting the information from original channel 1 and for slice 57 for example the info from channel 3, which is at least weird.

Because there are multiple Image IO backends. Can you check if using TIffImages directly works?

using TiffImages
TiffImages.load(filepath)

Yeah I've tried loading with TiffImages backend and the probelm stills.

If it is still the all-zero case, there might be some issues with your specific image file and TiffImages. In that case, providing an example image would be helpful to diagnose.

If you don't mind I can send you the image I am trying to load and I will be very grateful if you could help me.

https://drive.google.com/file/d/1JEDVJXh6yV5V5WU7qyvk_xBd4E1_rInJ/view?usp=sharing

Thanks in advance!

Originally posted by @DiegoPerezDones in JuliaImages/Images.jl#998 (comment)
@tlnagy tlnagy added the bug Something isn't working label Feb 17, 2022
@johnnychen94 johnnychen94 mentioned this issue Feb 17, 2022
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@DiegoPerezDones
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First of all, thanks in advance. The image is supposed to be a 3-channel hyperstack with 84 slices, each of them of 678x647 pixels, as @johnnychen94 noticed, but each channel it's not RGB but gray-scale inteisty values.

@tlnagy
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tlnagy commented Feb 17, 2022 •
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So I got a chance to play around with the image and this seemed to work:

using TiffImages
a = TiffImages.load("channels_24_1_R1.5.tif");

# convert to Gray to discard useless green and blue channels (all info is in red)
# and reshape since the color info is intercalated in the z dimension
b = reshape(Gray.(a), size(a)[[1,2]]..., 3, :)

# construct a new color view so now green and blue have the correct info
c = colorview(RGB, [view(b, :, :, i, :) for i in 1:3]...);

image

@tlnagy
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tlnagy commented Feb 17, 2022

But this is clearly a bug with TiffImages since it doesn't successfully detect the following:

  • It appears that the color info is spread across separate slices (!?) 1
  • It's actually 8bit, not 16bit
  • There's a colormap?
  • The TIFF is also MSB so the bits order needs to be flipped2

Footnotes

  1. I've never seen a TIFF do this. Truly bizarre. ↩

  2. This might be the source of some of the problems ↩

@tlnagy
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tlnagy commented Feb 17, 2022

ImageMagick reports the image as

  • A palette color image
  • MSB endianness
  • Depth at 8/16-bit (??)
  • Channel depth at 15, 1, 1 bits for RGB (wtf?)
Details 

Image:
  Filename: channels_24_1_R1.5.tif
  Format: TIFF (Tagged Image File Format)
  Mime type: image/tiff
  Class: PseudoClass
  Geometry: 678x647+0+0
  Units: PixelsPerInch
  Colorspace: sRGB
  Type: Palette
  Endianness: MSB
  Depth: 8/16-bit
  Channel depth:
    red: 15-bit
    green: 1-bit
    blue: 1-bit
  Channel statistics:
    Pixels: 438666
    Red:
      min: 0  (0)
      max: 61 (0.238285)
      mean: 3.668 (0.0143843)
      standard deviation: 8.23963 (0.0323123)
      kurtosis: 6.76108
      skewness: 2.57928
      entropy: 0.3491
    Green:
      min: 0  (0)
      max: 0 (0)
      mean: 0 (0)
      standard deviation: 0 (0)
      kurtosis: -3
      skewness: 0
      entropy: 0
    Blue:
      min: 0  (0)
      max: 0 (0)
      mean: 0 (0)
      standard deviation: 0 (0)
      kurtosis: -3
      skewness: 0
      entropy: 0
  Image statistics:
    Overall:
      min: 0  (0)
      max: 61 (0.238285)
      mean: 1.22267 (0.00479477)
      standard deviation: 2.74654 (0.0107708)
      kurtosis: 28.2718
      skewness: 5.01711
      entropy: 0.116367
  Colors: 62
  Histogram:
    330859: (0,0,0) #000000 black
    5347: (0.996109,0,0) #010000 srgb(0.390631%,0%,0%)
    3955: (1.99222,0,0) #020000 srgb(0.781262%,0%,0%)
    4732: (2.98833,0,0) #030000 srgb(1.17189%,0%,0%)
    4274: (3.98444,0,0) #040000 srgb(1.56252%,0%,0%)
    4758: (4.98054,0,0) #050000 srgb(1.95315%,0%,0%)
    4169: (5.97665,0,0) #060000 srgb(2.34379%,0%,0%)
    4201: (6.97276,0,0) #070000 srgb(2.73442%,0%,0%)
    4228: (7.96887,0,0) #080000 srgb(3.12505%,0%,0%)
    4122: (8.96498,0,0) #090000 srgb(3.51568%,0%,0%)
    3636: (9.96109,0,0) #0A0000 srgb(3.90631%,0%,0%)
    3619: (10.9572,0,0) #0B0000 srgb(4.29694%,0%,0%)
    4313: (11.9533,0,0) #0C0000 srgb(4.68757%,0%,0%)
    3831: (12.9494,0,0) #0D0000 srgb(5.0782%,0%,0%)
    3267: (13.9455,0,0) #0E0000 srgb(5.46883%,0%,0%)
    3240: (14.9416,0,0) #0F0000 srgb(5.85946%,0%,0%)
    3019: (15.9377,0,0) #100000 srgb(6.2501%,0%,0%)
    3345: (16.9339,0,0) #110000 srgb(6.64073%,0%,0%)
    2894: (17.93,0,0) #120000 srgb(7.03136%,0%,0%)
    3035: (18.9261,0,0) #130000 srgb(7.42199%,0%,0%)
    2874: (19.9222,0,0) #140000 srgb(7.81262%,0%,0%)
    3086: (20.9183,0,0) #150000 srgb(8.20325%,0%,0%)
    2900: (21.9144,0,0) #160000 srgb(8.59388%,0%,0%)
    2543: (22.9105,0,0) #170000 srgb(8.98451%,0%,0%)
    2425: (23.9066,0,0) #180000 srgb(9.37514%,0%,0%)
    2850: (24.9027,0,0) #190000 srgb(9.76577%,0%,0%)
    1975: (25.8988,0,0) #1A0000 srgb(10.1564%,0%,0%)
    1911: (26.8949,0,0) #1B0000 srgb(10.547%,0%,0%)
    1707: (27.8911,0,0) #1C0000 srgb(10.9377%,0%,0%)
    1654: (28.8872,0,0) #1D0000 srgb(11.3283%,0%,0%)
    1214: (29.8833,0,0) #1E0000 srgb(11.7189%,0%,0%)
    1174: (30.8794,0,0) #1F0000 srgb(12.1096%,0%,0%)
    922: (31.8755,0,0) #200000 srgb(12.5002%,0%,0%)
    725: (32.8716,0,0) #210000 srgb(12.8908%,0%,0%)
    551: (33.8677,0,0) #220000 srgb(13.2815%,0%,0%)
    649: (34.8638,0,0) #230000 srgb(13.6721%,0%,0%)
    533: (35.8599,0,0) #240000 srgb(14.0627%,0%,0%)
    658: (36.856,0,0) #250000 srgb(14.4533%,0%,0%)
    675: (37.8521,0,0) #260000 srgb(14.844%,0%,0%)
    439: (38.8482,0,0) #270000 srgb(15.2346%,0%,0%)
    329: (39.8444,0,0) #280000 srgb(15.6252%,0%,0%)
    336: (40.8405,0,0) #290000 srgb(16.0159%,0%,0%)
    366: (41.8366,0,0) #2A0000 srgb(16.4065%,0%,0%)
    236: (42.8327,0,0) #2B0000 srgb(16.7971%,0%,0%)
    42: (43.8288,0,0) #2C0000 srgb(17.1878%,0%,0%)
    169: (44.8249,0,0) #2D0000 srgb(17.5784%,0%,0%)
    17: (45.821,0,0) #2E0000 srgb(17.969%,0%,0%)
    67: (46.8171,0,0) #2F0000 srgb(18.3597%,0%,0%)
    119: (47.8132,0,0) #300000 srgb(18.7503%,0%,0%)
    196: (48.8093,0,0) #310000 srgb(19.1409%,0%,0%)
    95: (49.8054,0,0) #320000 srgb(19.5315%,0%,0%)
    22: (50.8016,0,0) #330000 srgb(19.9222%,0%,0%)
    22: (51.7977,0,0) #340000 srgb(20.3128%,0%,0%)
    25: (52.7938,0,0) #350000 srgb(20.7034%,0%,0%)
    19: (53.7899,0,0) #360000 srgb(21.0941%,0%,0%)
    21: (54.786,0,0) #370000 srgb(21.4847%,0%,0%)
    35: (55.7821,0,0) #380000 srgb(21.8753%,0%,0%)
    29: (56.7782,0,0) #390000 srgb(22.266%,0%,0%)
    66: (57.7743,0,0) #3A0000 srgb(22.6566%,0%,0%)
    10: (58.7704,0,0) #3B0000 srgb(23.0472%,0%,0%)
    99: (59.7665,0,0) #3C0000 srgb(23.4379%,0%,0%)
    37: (60.7626,0,0) #3D0000 srgb(23.8285%,0%,0%)
  Colormap entries: 256
  Colormap:
    0: (0,0,0) #000000 black
    1: (0.390631%,0%,0%) #010000 srgb(0.390631%,0%,0%)
    2: (0.781262%,0%,0%) #020000 srgb(0.781262%,0%,0%)
    3: (1.17189%,0%,0%) #030000 srgb(1.17189%,0%,0%)
    4: (1.56252%,0%,0%) #040000 srgb(1.56252%,0%,0%)
    5: (1.95315%,0%,0%) #050000 srgb(1.95315%,0%,0%)
    6: (2.34379%,0%,0%) #060000 srgb(2.34379%,0%,0%)
    7: (2.73442%,0%,0%) #070000 srgb(2.73442%,0%,0%)
    8: (3.12505%,0%,0%) #080000 srgb(3.12505%,0%,0%)
    9: (3.51568%,0%,0%) #090000 srgb(3.51568%,0%,0%)
    10: (3.90631%,0%,0%) #0A0000 srgb(3.90631%,0%,0%)
    11: (4.29694%,0%,0%) #0B0000 srgb(4.29694%,0%,0%)
    12: (4.68757%,0%,0%) #0C0000 srgb(4.68757%,0%,0%)
    13: (5.0782%,0%,0%) #0D0000 srgb(5.0782%,0%,0%)
    14: (5.46883%,0%,0%) #0E0000 srgb(5.46883%,0%,0%)
    15: (5.85946%,0%,0%) #0F0000 srgb(5.85946%,0%,0%)
    16: (6.2501%,0%,0%) #100000 srgb(6.2501%,0%,0%)
    17: (6.64073%,0%,0%) #110000 srgb(6.64073%,0%,0%)
    18: (7.03136%,0%,0%) #120000 srgb(7.03136%,0%,0%)
    19: (7.42199%,0%,0%) #130000 srgb(7.42199%,0%,0%)
    20: (7.81262%,0%,0%) #140000 srgb(7.81262%,0%,0%)
    21: (8.20325%,0%,0%) #150000 srgb(8.20325%,0%,0%)
    22: (8.59388%,0%,0%) #160000 srgb(8.59388%,0%,0%)
    23: (8.98451%,0%,0%) #170000 srgb(8.98451%,0%,0%)
    24: (9.37514%,0%,0%) #180000 srgb(9.37514%,0%,0%)
    25: (9.76577%,0%,0%) #190000 srgb(9.76577%,0%,0%)
    26: (10.1564%,0%,0%) #1A0000 srgb(10.1564%,0%,0%)
    27: (10.547%,0%,0%) #1B0000 srgb(10.547%,0%,0%)
    28: (10.9377%,0%,0%) #1C0000 srgb(10.9377%,0%,0%)
    29: (11.3283%,0%,0%) #1D0000 srgb(11.3283%,0%,0%)
    30: (11.7189%,0%,0%) #1E0000 srgb(11.7189%,0%,0%)
    31: (12.1096%,0%,0%) #1F0000 srgb(12.1096%,0%,0%)
    32: (12.5002%,0%,0%) #200000 srgb(12.5002%,0%,0%)
    33: (12.8908%,0%,0%) #210000 srgb(12.8908%,0%,0%)
    34: (13.2815%,0%,0%) #220000 srgb(13.2815%,0%,0%)
    35: (13.6721%,0%,0%) #230000 srgb(13.6721%,0%,0%)
    36: (14.0627%,0%,0%) #240000 srgb(14.0627%,0%,0%)
    37: (14.4533%,0%,0%) #250000 srgb(14.4533%,0%,0%)
    38: (14.844%,0%,0%) #260000 srgb(14.844%,0%,0%)
    39: (15.2346%,0%,0%) #270000 srgb(15.2346%,0%,0%)
    40: (15.6252%,0%,0%) #280000 srgb(15.6252%,0%,0%)
    41: (16.0159%,0%,0%) #290000 srgb(16.0159%,0%,0%)
    42: (16.4065%,0%,0%) #2A0000 srgb(16.4065%,0%,0%)
    43: (16.7971%,0%,0%) #2B0000 srgb(16.7971%,0%,0%)
    44: (17.1878%,0%,0%) #2C0000 srgb(17.1878%,0%,0%)
    45: (17.5784%,0%,0%) #2D0000 srgb(17.5784%,0%,0%)
    46: (17.969%,0%,0%) #2E0000 srgb(17.969%,0%,0%)
    47: (18.3597%,0%,0%) #2F0000 srgb(18.3597%,0%,0%)
    48: (18.7503%,0%,0%) #300000 srgb(18.7503%,0%,0%)
    49: (19.1409%,0%,0%) #310000 srgb(19.1409%,0%,0%)
    50: (19.5315%,0%,0%) #320000 srgb(19.5315%,0%,0%)
    51: (19.9222%,0%,0%) #330000 srgb(19.9222%,0%,0%)
    52: (20.3128%,0%,0%) #340000 srgb(20.3128%,0%,0%)
    53: (20.7034%,0%,0%) #350000 srgb(20.7034%,0%,0%)
    54: (21.0941%,0%,0%) #360000 srgb(21.0941%,0%,0%)
    55: (21.4847%,0%,0%) #370000 srgb(21.4847%,0%,0%)
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    58: (22.6566%,0%,0%) #3A0000 srgb(22.6566%,0%,0%)
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    60: (23.4379%,0%,0%) #3C0000 srgb(23.4379%,0%,0%)
    61: (23.8285%,0%,0%) #3D0000 srgb(23.8285%,0%,0%)
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    68: (26.5629%,0%,0%) #440000 srgb(26.5629%,0%,0%)
    69: (26.9535%,0%,0%) #450000 srgb(26.9535%,0%,0%)
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    85: (33.2036%,0%,0%) #550000 srgb(33.2036%,0%,0%)
    86: (33.5943%,0%,0%) #560000 srgb(33.5943%,0%,0%)
    87: (33.9849%,0%,0%) #570000 srgb(33.9849%,0%,0%)
    88: (34.3755%,0%,0%) #580000 srgb(34.3755%,0%,0%)
    89: (34.7662%,0%,0%) #590000 srgb(34.7662%,0%,0%)
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    92: (35.938%,0%,0%) #5C0000 srgb(35.938%,0%,0%)
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    147: (57.4228%,0%,0%) #920000 srgb(57.4228%,0%,0%)
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    242: (94.5327%,0%,0%) #F10000 srgb(94.5327%,0%,0%)
    243: (94.9233%,0%,0%) #F20000 srgb(94.9233%,0%,0%)
    244: (95.314%,0%,0%) #F30000 srgb(95.314%,0%,0%)
    245: (95.7046%,0%,0%) #F40000 srgb(95.7046%,0%,0%)
    246: (96.0952%,0%,0%) #F50000 srgb(96.0952%,0%,0%)
    247: (96.4858%,0%,0%) #F60000 srgb(96.4858%,0%,0%)
    248: (96.8765%,0%,0%) #F70000 srgb(96.8765%,0%,0%)
    249: (97.2671%,0%,0%) #F80000 srgb(97.2671%,0%,0%)
    250: (97.6577%,0%,0%) #F90000 srgb(97.6577%,0%,0%)
    251: (98.0484%,0%,0%) #FA0000 srgb(98.0484%,0%,0%)
    252: (98.439%,0%,0%) #FB0000 srgb(98.439%,0%,0%)
    253: (98.8296%,0%,0%) #FC0000 srgb(98.8296%,0%,0%)
    254: (99.2203%,0%,0%) #FD0000 srgb(99.2203%,0%,0%)
    255: (99.6109%,0%,0%) #FE0000 srgb(99.6109%,0%,0%)
  Rendering intent: Perceptual
  Gamma: 0.454545
  Chromaticity:
    red primary: (0.64,0.33)
    green primary: (0.3,0.6)
    blue primary: (0.15,0.06)
    white point: (0.3127,0.329)
  Background color: white
  Border color: srgb(223,223,223)
  Matte color: grey74
  Transparent color: black
  Interlace: None
  Intensity: Undefined
  Compose: Over
  Page geometry: 678x647+0+0
  Dispose: Undefined
  Iterations: 0
  Scene: 0 of 252
  Compression: None
  Orientation: TopLeft
  Properties:
    comment: ImageJ=1.53c
images=252
channels=3
slices=84
hyperstack=true
mode=composite
loop=false

    date:create: 2022-02-17T18:30:42+00:00
    date:modify: 2022-02-17T18:30:41+00:00
    signature: f74a7505cdc2b58e57bd1d0141cc4a80f77124642ce9a49c1103d619b95dbe3a
    tiff:alpha: unspecified
    tiff:endian: msb
    tiff:photometric: palette
    tiff:rows-per-strip: 12
  Artifacts:
    filename: channels_24_1_R1.5.tif
    verbose: true
  Tainted: False
  Filesize: 105.46MiB
  Number pixels: 438666
  Pixels per second: 897448B
  User time: 0.490u
  Elapsed time: 0:01.488
  Version: ImageMagick 6.9.11-60 Q16 x86_64 2021-01-25 https://imagemagick.org

@chrstphrbrns
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I've opened this file with Ubuntu's Document Viewer, Mac's Preview, and Mathematica, and they all appear to interpret the data the same way as TiffImages--as a sequence of 252 red-only images

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@tlnagy @chrstphrbrns @DiegoPerezDones