Problems with generating ome.tiffs with python script

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Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
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MalteLehmann
Posts: 3
Joined: Fri Dec 20, 2019 1:29 pm

Problems with generating ome.tiffs with python script

Post by MalteLehmann » Fri Dec 20, 2019 1:43 pm

Hey,
I am trying to use the python script in the jupyter notebook as shown in the IMC workshop. However in the last step I get error messages:

ERROR:root:Error in STARFim_20191211_OT1_s1_p6_r1_a1_ac.ome.tiff
Traceback (most recent call last):
File "<timed exec>", line 13, in <module>
File "C:\Users\Malte\Anaconda3\envs\imctools\lib\site-packages\imctools\scripts\ometiff2analysis.py", line 38, in ometiff_2_analysis
writer = imc_img.get_image_writer(outname + '.tiff', metals=selmetals, mass=selmass)
File "C:\Users\Malte\Anaconda3\envs\imctools\lib\site-packages\imctools\io\imcacquisition.py", line 39, in get_image_writer
order = self.get_metal_indices(metals)
File "C:\Users\Malte\Anaconda3\envs\imctools\lib\site-packages\imctools\io\imcacquisitionbase.py", line 91, in get_metal_indices
return [order_dict[m] for m in metallist]
File "C:\Users\Malte\Anaconda3\envs\imctools\lib\site-packages\imctools\io\imcacquisitionbase.py", line 91, in <listcomp>
return [order_dict[m] for m in metallist]
KeyError: '191Ir'
ERROR:root:Error in STARFim_20191211_OT1_s1_p6_r1_a1_ac.ome.tiff
Traceback (most recent call last):
File "<timed exec>", line 13, in <module>
File "C:\Users\Malte\Anaconda3\envs\imctools\lib\site-packages\imctools\scripts\ometiff2analysis.py", line 38, in ometiff_2_analysis
writer = imc_img.get_image_writer(outname + '.tiff', metals=selmetals, mass=selmass)
File "C:\Users\Malte\Anaconda3\envs\imctools\lib\site-packages\imctools\io\imcacquisition.py", line 39, in get_image_writer
order = self.get_metal_indices(metals)
File "C:\Users\Malte\Anaconda3\envs\imctools\lib\site-packages\imctools\io\imcacquisitionbase.py", line 91, in get_metal_indices
return [order_dict[m] for m in metallist]
File "C:\Users\Malte\Anaconda3\envs\imctools\lib\site-packages\imctools\io\imcacquisitionbase.py", line 91, in <listcomp>
return [order_dict[m] for m in metallist]
KeyError: '143Nd'

Now it says that getting a similar message like this might happen if I choose channels that have not actually been measured. These channels have been measured though and they do contain data. Does anybody know what I can change to make it work?

Thanks,

Malte
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