Open tlnagy opened 2 years ago
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:
[^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
``` 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%) 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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
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.
Yeah I've tried loading with TiffImages backend and the probelm stills.
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
Originally posted by @DiegoPerezDones in https://github.com/JuliaImages/Images.jl/issues/998#issuecomment-1041288642