You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Is your feature request related to a problem? Please describe.
This is a feature request I believe:
I would like to be able to run cellpose on the command line so that the diameter was estimated as in the GUI with the calibrate buttom. Otherwsie I have to load and image in the GUI, calibrate it, and then run all my images (from the same dataset) with the diameter from that single image I used for the calibration.
Describe the solution you'd like
To have a --calibrate boolean option that calibrates the image when enabled
Describe alternatives you've considered
According to the documentation I thought that setting the --diameter 0 would force the estimation of the diameter
--diameter
cell diameter, if 0 will use the diameter of the training labels used in the model, or with built-in model will estimate diameter for each image
However setting --diameter 0 actually produces an error when running cellpose. This is the full traceback
Traceback (most recent call last):
File "C:\Users\malieva\miniconda3\envs\cellpose\lib\runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "C:\Users\malieva\miniconda3\envs\cellpose\lib\runpy.py", line 86, in _run_code
exec(code, run_globals)
File "C:\Users\malieva\miniconda3\envs\cellpose\lib\site-packages\cellpose\__main__.py", line 358, in <module>
main()
File "C:\Users\malieva\miniconda3\envs\cellpose\lib\site-packages\cellpose\__main__.py", line 205, in main
out = model.eval(
File "C:\Users\malieva\miniconda3\envs\cellpose\lib\site-packages\cellpose\models.py", line 187, in eval
diams, _ = self.sz.eval(x, channels=channels, channel_axis=channel_axis,
File "C:\Users\malieva\miniconda3\envs\cellpose\lib\site-packages\cellpose\models.py", line 773, in eval
diam_style = self.diam_mean if (diam_style == 0 or
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
Thanks
Jorge
The text was updated successfully, but these errors were encountered:
Is your feature request related to a problem? Please describe.
This is a feature request I believe:
I would like to be able to run cellpose on the command line so that the
diameter
was estimated as in the GUI with thecalibrate
buttom. Otherwsie I have to load and image in the GUI, calibrate it, and then run all my images (from the same dataset) with the diameter from that single image I used for the calibration.Describe the solution you'd like
To have a
--calibrate
boolean option that calibrates the image when enabledDescribe alternatives you've considered
According to the documentation I thought that setting the
--diameter 0
would force the estimation of the diameter--diameter
cell diameter, if 0 will use the diameter of the training labels used in the model, or with built-in model will estimate diameter for each image
However setting
--diameter 0
actually produces an error when running cellpose. This is the full tracebackThanks
Jorge
The text was updated successfully, but these errors were encountered: