使用 ImageJ 或 ImageJ 在线查看的 C# 库无法查看图像已尝试 ImageMagick 和 ImageSharp 和 System.Drawing

Question

I have a file that I can view in ImageJ but most software just shows it in black. I am trying to view it in C# but it just comes up black, it is also not viewable in paint but I can view it in INcarta and ImageJ. The file is a 16 bit tiff that seems to have LZW compression

I am trying to use ImageSharp to decode this image and then show it as a bitmap. Here is a link to the file https://drive.google.com/file/d/16Xotc-2CJ6HkEJDysfKBkjClkU1OGiyQ/view?usp=sharing

    byte[] data = File.ReadAllBytes(fileToDisplay1);
    
 

            SixLabors.ImageSharp.Formats.Tiff.TiffDecoder decoder = new SixLabors.ImageSharp.Formats.Tiff.TiffDecoder();
            SixLabors.ImageSharp.Formats.Tiff.TiffEncoder encoder = new SixLabors.ImageSharp.Formats.Tiff.TiffEncoder();
            SixLabors.ImageSharp.Image? image = SixLabors.ImageSharp.Image.Load(data, decoder);




            System.Drawing.Bitmap bMap;
            using (var ms = new MemoryStream())
            {
                image.Save(ms, encoder);
                bMap = new Bitmap(ms);
            }

I have also tried ImageMagickQ16

byte[] data = File.ReadAllBytes(fileToDisplay1);
                
                var decoder = new SixLabors.ImageSharp.Formats.Tiff.TiffDecoder();
                var encoder = new SixLabors.ImageSharp.Formats.Tiff.TiffEncoder();
                //encoder.BitsPerPixel = SixLabors.ImageSharp.Formats.Tiff.TiffBitsPerPixel.Bit16;
                var image = SixLabors.ImageSharp.Image.Load(data, decoder);
                MagickImage im2;



               using (var ms = new MemoryStream())
                {
                    image.Save(ms, encoder);
                    im2 = new MagickImage(ms.ToArray());
                }



               //im2.Depth = 16;
                //im2.Grayscale();
                im2.AutoLevel();



               return im2.ToBitmap();

The File Looks like this: in ImageJ but is black when I upload it or when I try to use other software.

II have commented out other things I have tried

Answer 1

Imagemagick identify -verbose thinks your data is binary, just black and white. So there is some error in Imagemagick.

Image:
  Filename: mystery.tif
  Format: TIFF (Tagged Image File Format)
  Mime type: image/tiff
  Class: DirectClass
  Geometry: 2040x2040+0+0
  Units: PixelsPerInch
  Colorspace: Gray
  Type: Bilevel
  Base type: Grayscale
  Endianness: LSB
  Depth: 16/1-bit
  Channel depth:
    gray: 1-bit
  Channel statistics:
    Pixels: 4161600
    Gray:
      min: 0  (0)
      max: 0 (0)
      mean: 0 (0)
      standard deviation: 0 (0)
      kurtosis: -3
      skewness: 0
      entropy: 0
  Colors: 1
  Histogram:
       4161600: (0,0,0) #000000000000 gray(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: gray(255)
  Border color: gray(223)
  Matte color: gray(189)
  Transparent color: gray(0)
  Interlace: None
  Intensity: Undefined
  Compose: Over
  Page geometry: 2040x2040+0+0
  Dispose: Undefined
  Iterations: 0
  Compression: LZW
  Orientation: TopLeft
  Properties:
    date:create: 2022-09-27T00:43:06+00:00
    date:modify: 2022-09-27T00:42:39+00:00
    date:timestamp: 2022-09-27T00:43:25+00:00
    signature: 28f00fa3c1987b7b8f92961ef3a2d442cca23dbbb7c568b8908cc2fa2271de60
    tiff:alpha: unspecified
    tiff:endian: lsb
    tiff:photometric: min-is-black
  Artifacts:
    filename: mystery.tif
    verbose: true
  Tainted: False
  Filesize: 48240B
  Number pixels: 4161600
  Pixels per second: 84.8629MB
  User time: 0.060u
  Elapsed time: 0:01.049
  Version: ImageMagick 6.9.12-64 Q16 aarch64 17467 https://legacy.imagemagick.org

Mac Preview, GraphicConverter and Photoshop can read your image, but the gray levels are very low for a 16-bit range. Thus they appear at first glance as black. If the image dynamic range is stretched, the features show up.

But this does not work with Imagemagick since it thinks the data is binary and as such all the data values being very low have been put into the black bin.

Post and error to the Imagemagick web site at https://github.com/ImageMagick/ImageMagick/issues

This is either a bug in Imagemagick or your file is malformed according to the tiff documentation. The IM developers will need to decide which.

Answer 2

By default, the TiffDecoder will decode images as Rgba32 when using the non-generic API, ( something we can look into updating for v3 based upon the bit depth ), so you will not be capturing the image information since you are squashing 16bpp info into 8bpp.

Currently you can use Image.Identify(...) to determine the correct bit depth and make intelligent decoding choices, however, given that you know this image is grayscale and has a high dynamic range let's just decode it using L16 ( 16bit single luminance component ) and then stretch the histogram using the newly added method for V3. https://github.com/SixLabors/ImageSharp/pull/2235

using Image<La16> image = Image.Load<La16>(...);
image.Mutate(x => x.HistogramEqualization(new()
{
    LuminanceLevels = 65536,
    Method = HistogramEqualizationMethod.AutoLevel
}));
image.SaveAsPng(...)

The result is as expected.

PM> Install-Package SixLabors.ImageSharp -Version 3.0.0-alpha.0.52 -Source https://www.myget.org/F/sixlabors/api/v3/index.json