[ome-devel] Tiled TIFF import bug

[Melissa Linkert]

Hi Chris,

> I've recently found that Bio-Formats 4.4.7 and newer incorrectly
> read the TIFF images created by LI-COR Image Studio.  Although the
> images are read, the pixels are scrambled.  The last version to work
> was 4.4.6.
> 
> The problem is not limited to the Image Studio files.  Other tiled
> TIFF images can also trigger the bug.
> 
> A git bisect between v4.4.6 and v4.4.7 quickly found the problem commit:

Thank you for reporting this, and for uploading sample images.  We are
in the process of reviewing a fix:

http://github.com/openmicroscopy/bioformats/pull/871

I expect that this fix will be included in the upcoming 5.0.0 release.

Regards,
-Melissa

On Wed, Jan 29, 2014 at 02:50:05PM -0600, Chris Lesiak wrote:
> I've recently found that Bio-Formats 4.4.7 and newer incorrectly
> read the TIFF images created by LI-COR Image Studio.  Although the
> images are read, the pixels are scrambled.  The last version to work
> was 4.4.6.
> 
> The problem is not limited to the Image Studio files.  Other tiled
> TIFF images can also trigger the bug.
> 
> A git bisect between v4.4.6 and v4.4.7 quickly found the problem commit:
> 
> 
> 64f33a89e3277a5c9a6d1bb6cbcd546e6f3a9b95 is the first bad commit
> commit 64f33a89e3277a5c9a6d1bb6cbcd546e6f3a9b95
> Author: Melissa Linkert <melissa at glencoesoftware.com>
> Date:   Mon Mar 4 12:52:01 2013 -0500
> 
>     TIFF: adjust the optimal tile height for large single-tile images
> 
>     See
> http://lists.openmicroscopy.org.uk/pipermail/ome-users/2013-March/003597.html
>     and
> http://lists.openmicroscopy.org.uk/pipermail/ome-users/2013-March/003601.html
> 
> :040000 040000 13d5049c3cb421dbc95eb6f3f76e6d4b549d73fa
> 44df26899b2b7612e82bcaef719a1c89f2bfc956 M    components
> 
> 
> 
> I've uploaded the following test images:
> 
> cramps-tile.tif    This image (from pics-3.8.0.tar.gz) doesn't
> trigger the bug because the photometric interpretation is
> min-is-white.
> 
> cramps-tile-min-is-black.tif    This image is identical to
> cramps-tile.tif except I've changed the photometric interpretation
> to min-is-black.  It triggers the bug.
> 
> tiled-pyramid-half-hdr.tiff    This image generated by Image Studio
> also triggers the bug.  The image has a background of 0 with an an
> array of 40 pixel diameter spots exercising the full range of a
> 16-bit float, including NaN, +Inf, and -Inf.
> 
> 
> -- 
> Chris Lesiak
> Principal Design Engineer, Software
> LI-COR, Inc.
> chris.lesiak at licor.com
> 
> Any opinions expressed are those of the author and
> do not necessarily represent those of his employer.
> 
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