Resolved: Issue reading non-square ImageJ BigStacks about tiffstack HOT 6 CLOSED

Please let me know the exact dimensions of your stack, if possible. Also let me know what version of ImageJ you have, and please check you are using the latest versions of TIFFStack and MappedTensor.

from tiffstack.

I have just fixed a bug in TIFFStack where the number of frames, channels, slices would be set incorrectly, since ImageJ doesn't write these values out if they are equal to 1. Please check to see if that fixes your issue.

from tiffstack.

Hi Dylan,

Thanks so much for the speedy reply. The stack has dimensions 512 x 672 x 9000 (rows,col,time).; ImageJ v1.49 ; just updated to latest version of TIFFStack and MappedTensor. Unfortunately, still running into the same problem. When I save the file in imageJ, I get the following info if I want to open the file as 'raw':
name=Untitled, dir=, width=672, height=512, nImages=9000, offset=304092, type=ushort, byteOrder=big, format=0, url=, whiteIsZero=f, lutSize=0, comp=1, ranges=null, samples=1

I've attached two .png files - the first is what the first frame should look like (:,:,1), the second is what the first frame of the TIFFobject in MATLAB looks like:

from tiffstack.

@raswanson Thanks for getting back to me. The issue was in constructing the MappedTensor to read the stack — the first two dimensions were incorrectly assigned, leading the image to be incorrectly shaped. I've just committed a fix; please check that everything looks good for you now, and reopen this issue if there are still problems.

Thanks for your help in fixing the bug!

from tiffstack.

Hi Dylan,

Your TiffStack function is working almost perfectly post the fix above - just one final problem I'd hugely appreciate help with!

TiffStack successfully loads tiff stacks > 4 GB and I can access this data via indexing into the created object, however when I access a single slice of the data (tiffstack(:,:,1)), the following warning prints 5 times:

Warning: TIFF library warning - 'TIFFReadDirectory: Unknown field with tag 65329 (0xff31) encountered.'

In TIFFStack>TS_set_directory (line 1550)
In TIFFStack>TS_read_data_Tiff (line 1245)
In TIFFStack/subsref (line 679)
In GridSmooth (line 57)

Because this prints for every slice along the z dimension (regardless of the number of pixels accessed within that frame), when I try to access large portions of the data it takes an unworkably long amount of time.

Again, any help is much appreciated!

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from tiffstack.