Windows x64 v9770 error when loading TIFs

I gave the v9770 x64 windows beta a try today and boy does it looks good. Great job. I’ve been able to run through our entire pipeline with only one minor problem.

CP2 is more picky about the tifs it can read. Our current process relies on takinga Nikon RAW image (NEF format) and converting it to a TIF using DCRaw or ufraw. There is a known bug in the DCRaw code where the tifs have “invalid TIFF direcory; tags are not sorted in ascending order.” GIMP is the only other program that complains about these files, but it is only an error message and the file opens and displays correctly. CP1 has no issue loading these tifs. Below are the errors that kick out when attempting to load the image and attached is an example “problem” tif.

Starting VM
VM started
Subversion revision: 9770
Exception in thread “Thread-1” java.lang.NullPointerException
at loci.formats.FormatReader.openBytes(
at loci.formats.FormatReader.openBytes(
at loci.formats.ImageReader.openBytes(
Traceback (most recent call last):
File “cellprofiler\modules\loadimages.pyc”, line 1760, in provide_image
File “cellprofiler\modules\loadimages.pyc”, line 1887, in load_using_bioformats
File “cellprofiler\utilities\jutil.pyc”, line 337, in method
File “cellprofiler\utilities\jutil.pyc”, line 276, in call
Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 302, in run
File “cellprofiler\modules\loadimages.pyc”, line 1350, in run
File “cellprofiler\modules\loadimages.pyc”, line 1763, in provide_image
File “cellprofiler\modules\loadimages.pyc”, line 1792, in load_using_PIL
File “contrib\tifffile.pyc”, line 208, in asarray
IndexError: list index out of range
Fri Apr 9 14:23:16 2010: Image # 1, module LoadImages # 1: 0.45 sec (bg)
C:\Program Files\CellProfiler\\cellprofiler\gui\
:373: DeprecationWarning: BaseException.message has been deprecated as of Python


We now use Bio-Formats to process various image formats. From the error message, it appears that the problem lies with Bio-Formats failing to interpret the image correctly. We have forwarded this issue plus the offending file to them, and I’ll post here when we hear back.


Version 9978 has just been released which now supports this file type.