How to save processed 3D image tiff file as tiff file again, with same tag information?

I load a 3D tiff image.

I processed the image.

Now I want to save the image again as tiff file, with the same information for imfinfo('image.tif')

How can I do that?

I want to save this information within the tiff file:

setTag(t,'FileModDate: '29-jan-2020 14:44:18'

FileSize: 84827

Format: 'tif'

FormatVersion: []

Width: 229

Height: 352

BitDepth: 8

ColorType: 'grayscale'

FormatSignature: [73 73 42 0]

ByteOrder: 'little-endian'

NewSubFileType: 0

BitsPerSample: 8

Compression: 'Uncompressed'

PhotometricInterpretation: 'BlackIsZero'

StripOffsets: []

SamplesPerPixel: 1

RowsPerStrip: 4.2950e+09

StripByteCounts: []

XResolution: 16.5657

YResolution: 24.0214

ResolutionUnit: 'Centimeter'

Colormap: []

PlanarConfiguration: 'Chunky'

TileWidth: 80

TileLength: 352

TileOffsets: [8 28168 56328]

TileByteCounts: [28160 28160 28160]

Orientation: 1

FillOrder: 1

GrayResponseUnit: 0.0100

MaxSampleValue: 254

MinSampleValue: 0

Thresholding: 1

Offset: 84488

ImageDescription: 'MeVisLab'

Software: 'MFL MeVis File Format Library, TIFF Module'

SampleFormat: 'Unsigned integer'

Answer 1

[Sai Sri Pathuri]

You may follow the steps below to save the processed image as Tiff file.

Create a Tiff object with ‘w’ mode to write the image data to a TIFF file.

t = Tiff('processedfile.tif','w'); 

For new tiff file to have the same information as existing tiff file, create a tag structure with fields having same values as existing file. Note that all the parameters of imfinfo cannot be set using this structure. You may refer properties section of Tiff documentation page for declaring the required fields of structure.

For example,

tagstruct. ImageLength = size(processedImage,1); 
tagstruct. ImageWidth = size(processedImage,2); 
tagstruct.PlanarConfiguration = Tiff.PlanarConfiguration.Chunky; 

Use setTag function to set the tag values to the new tiff file

setTag(t,tagstruct); 

Write the processed image into tiff file using write function

write(t,processedImage);  

You may also refer the examples in write function documentation for defining the tag structure and writing image to a tiff file

[Walter Roberson]

Although the above is generally good practice, it is not sufficient in practice. Tiff does not offer actual 3D images. What it does offer is a way to put several images into one file, and a rich tag structure that some software packages use to provide information to themselves about how the multiple images should fit together in 3D.

The most common 3d-as-such convention is one created by ImageJ

It might be the case that the most common 3d-in-practice convention is GeoTiff, which has an actual Standard created for it. GeoTiff is not intended for 3d as such: it is intended to be able to provide a lot of auxiliary data especially for maps, such as hyperspectral dat, or roads, or sewer systems, or whatever else might be desired by GIS, and along the way it also happens to provide a way to create 3d data.

Now, it happens that MeVisLab does not use either of these. Instead it uses the SGI 3D TIFF extension. I do not happen to find a reference for how that works at the moment. Also it uses 32 bit float. It also embeds a 16 bit integer DICOM image inside the TIFF image.

So... Because 3D in TIFF is not as simple as one might hope, then to hope to get things right when modifying the data, often it turns out to be easier to take a copy of the tiff file, and then use the Tiff() class to maneuver through the subimage directory, and replace the image data parts as appropriate. This process ensures that all of the tags are in the right place and are in the same order -- because proprietary setups like MeVisLab uses are often sensitive to all the details being in the same order, not just to all of the information being available in the header.

[M W]

Dear Roberson,

Thank you very much for the comprehensive answer.

My idea was also to replace the image data within a copy of the original tiff file, to preserve the tag structure.

Unfortunately, I can't find a way to do this.

To process and adapt the 3D image I load the tiff-file, by the function 'read'.

The image becomes a matrix and I make some changes.

After that, I try to replace the original tiff image with the processed version.

The problem is that it seems that I can't find a function to do this.

I tried, write(t, tiff), as mentioned above, but this creates a new tiff image.

How can I solve this problem? For example, is there a Matlab function that can overwrite tiff files, while preserving all tag structures. I may have missed this function in my search.

Thank you

[Walter Roberson]

In theory write() should only affect the current IFD.

[M W]

I tried the following:

%load tiff
t = Tiff('130193_whjo_rest.tif','r'); %read tiff
imf_mark = read(t);  %matrix of tiff image 
 
%process example 
kader_z=30; 
kader_r=30;
imf_mark((ind_r-kader_r):(ind_r+kader_r),ind_c,(ind_z+kader_z))=1;
imf_mark((ind_r+kader_r),ind_c,(ind_z-kader_z):(ind_z+kader_z))=1;
imf_mark((ind_r-kader_r):(ind_r+kader_r),ind_c,(ind_z-kader_z))=1;
imf_mark((ind_r-kader_r),ind_c,(ind_z-kader_z):(ind_z+kader_z))=1;
 
%overwrite  
write(t,imf_mark); %save processed image in save file  

This results in the following error:

Error using Tiff/writeAllTiles (line 2234)
SamplesPerPixel is 1, but the number of image planes provided was 277.
 
Error in Tiff/write (line 1480)
                obj.writeAllTiles(varargin{:});
                

Can you see what I do wrong? Or how I can resolve the error?

Thank you very much!

[Walter Roberson]

At each IFD, you need to write() data that is exactly the same size as the image that is present at that IFD.

There is more than one way to write 3D data to TIFF. One of the ways is to write a single image with a lot of ExtraSamples. That approach does not appear to be used much in practice for 3D images: it tends to be used more for hyperspectral data, where there is no conceptual "distance" between the panes. It is more common for 3D TIFF to be implemented as a TIFF file with multiple IFD, each of which is a single layer. That single layer might be grayscale (SamplesPerPixel is 1) or RGB (SamplesPerPixel is 3); the error message you received suggests that the TIFF file is storing each layer as seperate IFD entries.

[M W]

Thank you for your reaction.

I see your point.

First, I specified all tags manually, which resolved a number of errors.

However, after I added all the information I could extract from the original tiff file, more errors keep occurring.

Information is needed that I can't provide.

Therefore, I want to copy all specified information from the original tiff file and simply added to my adapted version.

Do you know a way to do that?

Thanks in advance.