TiffImages.jl
TiffImages.jl copied to clipboard
Published
20 hours ago •
tlnagy
tlnagy
Image is being incorrectly interpreted as 16bit instead of 8bit
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 https://github.com/JuliaImages/Images.jl/issues/998#issuecomment-1041288642
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.
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]...);
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 flipped[^2]
[^1]: I've never seen a TIFF do this. Truly bizarre. [^2]: This might be the source of some of the problems
ImageMagick reports the image as
- [x] A palette color image
- [x] MSB endianness
- [x] Depth at 8/16-bit (??)
- [x] 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%)
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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
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
