[BUG]aMap registration only in cellfinder with window10

Hi Adam, Thank you for releasing the cellfinder version with Window support. I’m trying to only register a brain sample that was already downsampled to isotropic 10um resolution, but error was reported in windows 10. 1, Basic testing with only detection worked fine, with a .xml file output with candidate cell coordinates. cellfinder -s "C:\Users\Steinmetz lab\Documents\amap_data\ERAE23_3c" -b "C:\Users\Steinmetz lab\Documents\amap_data\ERAE23_3c" -o "C:\Users\Steinmetz lab\Documents\amap_data\ERAE23_3c_output" -x 10 -y 10 -z 10 --no-classification 2, aMap registration only, failed with error message. cellfinder -s "C:\Users\Steinmetz lab\Documents\amap_data\ERAE23_3c" -b "C:\Users\Steinmetz lab\Documents\amap_data\ERAE23_3c" -o "C:\Users\Steinmetz lab\Documents\amap_data\ERAE23_3c_output" -x 10 -y 10 -z 10 --flip-x --register --no-detection --no-classification

2020-05-06 23:59:20 PM - INFO - MainProcess fancylog.py:265 - Starting logging Traceback (most recent call last): 2020-05-06 23:59:20 PM - INFO - MainProcess fancylog.py:267 - Multiprocessing-logging module found. Logging from all processes File “c:\users\steinmetz lab\appdata\local\programs\python\python37\lib\runpy.py”, line 193, in _run_module_as_main 2020-05-06 23:59:20 PM - INFO - MainProcess main.py:32 - Registering to atlas “main”, mod_spec)2020-05-06 23:59:20 PM - INFO - MainProcess prep.py:401 - Checking whether the atlas exists

File “c:\users\steinmetz lab\appdata\local\programs\python\python37\lib\runpy.py”, line 85, in run_code exec(code, run_globals) File "C:\Users\Steinmetz lab\AppData\Local\Programs\Python\Python37\Scripts\cellfinder.exe_main.py", line 7, in <module> File “c:\users\steinmetz lab\appdata\local\programs\python\python37\lib\site-packages\cellfinder\main.py”, line 61, in main debug=args.debug, File “c:\users\steinmetz lab\appdata\local\programs\python\python37\lib\site-packages\amap\main.py”, line 93, in main registration_config, dest_folder=Path(registration_output_folder) File “c:\users\steinmetz lab\appdata\local\programs\python\python37\lib\site-packages\amap\config\atlas.py”, line 25, in init super().init(config_path) File “c:\users\steinmetz lab\appdata\local\programs\python\python37\lib\site-packages\neuro\atlas\atlas_class.py”, line 24, in init atlas_id = list(data_dict.keys())[0] # assume only one key IndexError: list index out of range

Any ideas why this happened? I have ran “cellfinder_download” before hand to download atlas to default folders.

[adamltyson]

There’s an issue that amap and cellfinder don’t work properly together, so it will download two versions of the atlas (one at ~/.amap and one at ~/.cellfinder). If you want to prevent these both from existing, you should be able to delete the ~/.amap directory and then run amap_download --install-path ~/.cellfinder/atlas (or the Windows equivalent) to link them.

I’m not sure why registration in cellfinder isn’t working properly, I’ll look into it.

We should also add this to the tests (https://github.com/SainsburyWellcomeCentre/cellfinder/issues/93)

[adamltyson]

Closing this as I can’t seem to reproduce. @zhiwen10 feel free to reopen if this occurs again.