Changes between Initial Version and Version 1 of Ticket #1696

Timestamp:

Feb 11, 2019, 5:41:04 PM (7 years ago)

Author:

Tom Goddard

Comment:

I looked at the 5 Gbyte TIFF file you gave me and it indeed contains a single TIFF plane. It turns out that ImageJ hacks the TIFF format to handle data larger than 4 Gbytes. Instead of a single TIFF plane for each 2D plane of data, it puts all the data into one plane, with custom ImageJ TIFF header tags to tell a custom ImageJ reader how to extract all the actual planes from that single TIFF plane.

Here is an explanation of this hack from the Bioformats documentation

​https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/tiff.html

"TIFF files written by ImageJ are also supported, including ImageJ TIFFs larger than 4GB. ImageJ TIFFs are detected based upon the text in the first IFD’s “ImageDescription” tag; this tag’s value is then used to determine Z, C, and T sizes as well as physical sizes and timestamps. For ImageJ TIFFs larger than 4GB, a single IFD is expected (instead of one IFD per image plane). The “ImageDescription” is used to determine the number of images, the pixel data for which are expected to be stored contiguously at the offset indicated in the sole IFD. This differs from standard TIFF and BigTIFF; if the “ImageDescription” tag is missing or invalid, only the first image will be read."

ChimeraX uses the Python Image Library TIFF reader that of course does not have the custom code to extract the data that ImageJ crammed into a single plane. ChimeraX does read some custom ImageJ TIFF headers to know the number of z slices, channels and time points. But it does not have the special code to handle the > 4 Gbyte case where all the data is packed into a single plane.

ChimeraX could be enhanced to read this custom ImageJ use of TIFF.