I am currently trying to convert the following .vsi files into .tif files.
20180910_stimulated yfp_YFP-f_003_current
20180911_csf1after5min stimulated flms_PH_001_current
sad323-00a6ls04:untitled folder jared$ python -m microscoper --list
./20180910_stimulated yfp_YFP-f_003_current/stack1/20180910_stimulated yfp_YFP-f_003_current.vsi
./20180911_csf1after5min stimulated flms_PH_001_current/stack1/20180911_csf1after5min stimulated flms_PH_001_current.vsi
Total files found: 2
When I try to convert the following files into the tif format using the command python -m microscoper. I get the following output. One .tif file is created, but it gets stuck and doesn't process the rest of the files. I was able to get this working on my old macbook, but I recently got a new macbook and had to download it onto my new one, but I am having trouble getting it to work. I can open my files through imageJ using bioformats, but this can save me a lot of time to convert many files at once. Thanks
Traceback (most recent call last): | 0/2 [00:00<?, ?it/s]
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 174, in _run_module_as_main██████████| 100/100 [00:00<00:00, 102.77it/s]
"main", fname, loader, pkg_name)█████████| 1/1 [00:00<00:00, 127.46it/s]
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/Users/jared/microscoper/microscoper/main.py", line 3, in
run()
File "/Users/jared/microscoper/microscoper/io.py", line 212, in run
save_metadata(metadata, save_directory)
File "/Users/jared/microscoper/microscoper/io.py", line 138, in save_metadata
xmlfile.write(pretty_xml_as_string)
UnicodeEncodeError: 'ascii' codec can't encode character u'\xb5' in position 565: ordinal not in range(128)
I am currently trying to convert the following .vsi files into .tif files.
20180910_stimulated yfp_YFP-f_003_current
20180911_csf1after5min stimulated flms_PH_001_current
sad323-00a6ls04:untitled folder jared$ python -m microscoper --list
./20180910_stimulated yfp_YFP-f_003_current/stack1/20180910_stimulated yfp_YFP-f_003_current.vsi
./20180911_csf1after5min stimulated flms_PH_001_current/stack1/20180911_csf1after5min stimulated flms_PH_001_current.vsi
Total files found: 2
When I try to convert the following files into the tif format using the command python -m microscoper. I get the following output. One .tif file is created, but it gets stuck and doesn't process the rest of the files. I was able to get this working on my old macbook, but I recently got a new macbook and had to download it onto my new one, but I am having trouble getting it to work. I can open my files through imageJ using bioformats, but this can save me a lot of time to convert many files at once. Thanks
Traceback (most recent call last): | 0/2 [00:00<?, ?it/s]
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 174, in _run_module_as_main██████████| 100/100 [00:00<00:00, 102.77it/s]
"main", fname, loader, pkg_name)█████████| 1/1 [00:00<00:00, 127.46it/s]
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/Users/jared/microscoper/microscoper/main.py", line 3, in
run()
File "/Users/jared/microscoper/microscoper/io.py", line 212, in run
save_metadata(metadata, save_directory)
File "/Users/jared/microscoper/microscoper/io.py", line 138, in save_metadata
xmlfile.write(pretty_xml_as_string)
UnicodeEncodeError: 'ascii' codec can't encode character u'\xb5' in position 565: ordinal not in range(128)