Hi Adam! I have a couple of errors during visualization.
(1) While running
amap_vis "C:\Users\sthit\Documents\rabies_D2_ToS\out\registration" or cellfinder_region_summary "C:\Users\sthit\Documents\rabies_D2_ToS\out\registration"
File "c:\users\sthit\anaconda3\envs\cellfinder\lib\site-packages\imlib\source\source_files.py", line 29, in get_structures_path
atlas_conf = config_obj["atlas"]
File "c:\users\sthit\anaconda3\envs\cellfinder\lib\site-packages\configobj.py", line 554, in getitem
val = dict.getitem(self, key)
KeyError: 'atlas'
(2) While trying to save all layers from cellfinder visualizer,
File "c:\users\sthit\anaconda3\envs\cellfinder\lib\site-packages\napari\plugins\io.py", line 273, in _write_multiple_layers_with_plugins
raise PluginCallError(implementation, cause=exc)
napari_plugin_engine.exceptions.PluginCallError: Error in plugin 'builtins', hook 'napari_get_writer': Error in plugin 'builtins', hook 'napari_write_image'
brainreg /path/to/data /path/to/output -x 3.6498 -y 3.6498 -z 15.3767 --orientation lsp --atlas allen_mouse_25um
Hi!
I am having a problem with registering a brain for a current project. Right before the Debug process starts to run I receive this error:
Traceback (most recent call last):
File "c:\users\administrator\miniconda3\envs\cellfinder\lib\concurrent\futures\process.py", line 239, in _process_worker
r = call_item.fn(call_item.args, *call_item.kwargs)
File "c:\users\administrator\miniconda3\envs\cellfinder\lib\site-packages\brainio\brainio.py", line 465, in load_from_paths_sequence
return volume
UnboundLocalError: local variable 'volume' referenced before assignment
This error only occurs with this one brain. All other brains I register succeed. Thank you for your help!