How can I save a color 3D image bigger than 4 GB to a TIF file?

The Tiff class basically is capable of saving colored 3D images to a multi-page TIF. But the size of the image is limited to 4 GB, no matter how much space is available on hard disk. Function found in file exchange can save monochromatic 3D images or 2D color images only.

[Stephen23]

The TIFF file formats use 32-bit offsets which limits file size to around 4 GiB:

It is unclear why you expect the TIFF format to store more data than it is designed to do.

[ImageProcessingScientist]

Python does save images with more than 4 GB to TIF files.

[Stephen23]

"Python does save images with more than 4 GB to TIF files."

No, it does not:

1. Python (the programming language) supports no image importing or exporting or any image-data specific processing at all. Zilch. Nada. Nothing... there is nothing in the Python standard library nor in the Python language about images of any type (of course some third party libraries such as Pillow, scikit-image, tifffile and others certainly do support image file processing/importing/exporting, but clearly they are not Python).
2. The TIFF standard (written by Adobe, i.e. one of the companies who co-created the TIFF file format) states "The largest possible TIFF file is 2**32 bytes in length." Note that 2^32 is exactly 4 GiB, i.e. four gibibytes. You can read the TIFF standard here, which explicitly states the largest possible file size: https://web.archive.org/web/20210108073850/https://www.adobe.io/open/standards/TIFF.html

Of course TIFF is not the same as BigTIFF:

https://web.archive.org/web/20041211081128/https://www.awaresystems.be/imaging/tiff/bigtiff.html

Note that the introduction to the BigTIFF format proposal also states "The TIFF file format uses 32bit offsets and, as such, is limited to 4 gigabytes." Why they would state that? Hmmm, come to think of it, why would they put all of that effort into deriving the BigTIFF format to get around a limit which you (incorrectly) claim does not even exist?

So far every source of information written by reliable sources indicates that TIFF is limited to 4 GiB. But is it enough to merely trust the authors of the TIFF file standard? Not these days... so lets actually test some of those python libaries. Actually we can save some time by reading the Pillow documentation... oh, it states "Maximum pixel dimensions are limited to INT32, or 2^31 by the sizes in the image header.", which is about two gibibytes. So there is not point in trying Pillow (actually I did try it, it throws an error). Lets try tifffile, first with an image which is 2 bytes smaller than 4 GiB:

import numpy as np
import tifffile as tf
arr = np.random.randint(0, 256, size=2**32-2, dtype=np.uint8)
arr.nbytes
Out[4]: 4294967294
tf.imwrite('4GiB-2B.tiff', arr.reshape(2,-1), bigtiff=False) # 4 GiB - 2 B TIFF file

No error. Now lets try an image which is 2 bytes larger than 4 GiB:

arr = np.random.randint(0, 256, size=2**32+2, dtype=np.uint8)
arr.nbytes
Out[7]: 4294967298

tf.imwrite('4GiB+2B.tiff', arr.reshape(2,-1), bigtiff=False) # 4 GiB + 2 B TIFF file

Traceback (most recent call last):

Cell In[8], line 1
tf.imwrite('4GiB+2B.tiff', arr.reshape(2,-1), bigtiff=False)

File C:\WPy64-31241\python-3.12.4.amd64\Lib\site-packages\tifffile\tifffile.py:1299 in imwrite
result = tif.write(

File C:\WPy64-31241\python-3.12.4.amd64\Lib\site-packages\tifffile\tifffile.py:2981 in write
addtag(tags, tagbytecounts, bytecountformat, count, databytecounts)

File C:\WPy64-31241\python-3.12.4.amd64\Lib\site-packages\tifffile\tifffile.py:3840 in _addtag
ifdentry.append(pack(valueformat, pack(dataformat, value)))

File C:\WPy64-31241\python-3.12.4.amd64\Lib\site-packages\tifffile\tifffile.py:3866 in _pack
return struct.pack(fmt, *val)

error: 'I' format requires 0 <= number <= 4294967295

Oh, an error, just as expected (because what you claim is impossible). Just for fun (even though it is completely unrelated to your (incorrect) statement) lets also try writing that image to a BigTIFF file:

tf.imwrite('4GiB+2B.bigtiff', arr.reshape(2,-1), bigtiff=True) # BigTIFF file

No error there either, just as expected. (It is also worth noting that tifffile does automatically switch to BigTIFF for larger images if the bigtiff argument is not specified).

So far everything seems to indicate that TIFF files cannot be larger than 4 GiB. Nothing supports your claim that "Python does save images with more than 4 GB to TIF files". Can you provide any evidence to support it?

[ImageProcessingScientist]

If Python does not save TIFF files, because Scikit-Image is not Python, Matlab does not save these files either, because the Image Processing Toolbox is not Matlab. Image Processing without Image Processing Toolbox (Matlab) or Scikit-Image or OpenCV (both Python) is a challenging task to say the least.

[Stephen23]

According to https://scikit-image.org/ it is "... written by an active community of volunteers", so it is as much Python as your scripts or my scripts are. The fact that other people might use it does not somehow make it part of Python.

I agree that the Image Processing Toolbox is not MATLAB (it is created and distributed by TMW, who also create MATLAB).

Answer 1

[Walter Roberson]

https://www.mathworks.com/matlabcentral/fileexchange/42086-bigtiffwriter supports uint8 RGB images.

See also https://blogs.mathworks.com/steve/2013/08/07/tiff-bigtiff-and-blockproc/