Tiff montage problem using Python27 for Amnis .cif files

Dear image.sc users,

I was following the protocol for IFC data analysis published in a paper by Henning et. al with a further step-by-step explanation from CellProfiler homepage.

I had an issue previously, which was solved successfully by bcimini.

I had to come back and do some additional analysis of new data on the same pc and have a new problem. After running the stitching command for .cif file i get the following (and i am not exactly sure which is the real problem here the attribute error or NoneType objects):

C:\amnis\Stitching>python stitching -o C:\amnis\Example C:\amnis\example.cif
log4j:WARN No appenders could be found for logger (loci.common.NIOByteBufferProvider).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Traceback (most recent call last):
File “C:\Python27\lib\runpy.py”, line 174, in run_module_as_main
main”, fname, loader, pkg_name)
File “C:\Python27\lib\runpy.py”, line 72, in run_code
exec code in run_globals
File "C:\amnis\Stitching\stitching_main
.py", line 115, in
main()
File “C:\Python27\lib\site-packages\click\core.py”, line 764, in call
return self.main(*args, **kwargs)
File “C:\Python27\lib\site-packages\click\core.py”, line 717, in main
rv = self.invoke(ctx)
File “C:\Python27\lib\site-packages\click\core.py”, line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “C:\Python27\lib\site-packages\click\core.py”, line 555, in invoke
return callback(*args, **kwargs)
File "C:\amnis\Stitching\stitching_main
.py", line 29, in main
_stitch(image, output, image_size, montage_size)
File "C:\amnis\Stitching\stitching_main
.py", line 55, in __stitch
montage = skimage.util.montage.montage2d(numpy.asarray(images), 0)
AttributeError: ‘function’ object has no attribute ‘montage2d’
TypeError: ‘NoneType’ object is not callable
Exception TypeError: “‘NoneType’ object is not callable” in ‘_javabridge.JB_Object.dealloc’ ignored
TypeError: ‘NoneType’ object is not callable
Exception TypeError: “‘NoneType’ object is not callable” in ‘_javabridge.JB_Object.dealloc’ ignored
TypeError: ‘NoneType’ object is not callable
Exception TypeError: “‘NoneType’ object is not callable” in ‘_javabridge.JB_Object.dealloc’ ignored

Would be thankful for suggestions to deal with this.

problem solved by upgrading to a new version of the app:

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