I have the following problem. I want to save a tif file with numpy in python of a 3D array and open it with imageJ in a macro. The problem ist that, whenever I save it, and manually open it in ImageJ it is recognizes as a hyperstack. I think the problem is that the file is over 4GB, is that possible?
How are you saving the tif exactly?
Can you elaborate? Do you mean that ImageJ thinks the third axis is time (or channels?)
rather than a third spatial dimension?
If so, then I’d bet that however you’re writing the tiff is not saving metadata that ImageJ uses to interpret the 3rd (or 4th or 5th) dimension.
Ok, that could be. I saving them with io.imsave(‘test.tif’,array.astype(np.npunit16)), the problem is that I have to use the standard packages for python. If i do it with a smaller array, it works and imageJ open it as 3d stack.
What size does it work for and what for size does it fail?
I have to check this, maybe by creating random arrays. I think its when the file becomes larger than 4GB. Then it also has no information about x,y,z ranges in the properties of the files.