Merge branch 'main' of https://github.com/mouseland/cellpose

README.md

@@ -87,7 +87,7 @@ If you are using a GPU, make sure its drivers and the cuda libraries are correct
 
 1. Install an [Anaconda](https://www.anaconda.com/products/distribution) distribution of Python. Note you might need to use an anaconda prompt if you did not add anaconda to the path.
 2. Open an anaconda prompt / command prompt which has `conda` for **python 3** in the path
-3. Create a new environment with `conda create --name cellpose python=3.8`. We recommend python 3.8, but python 3.9 and 3.10 will likely work as well.
+3. Create a new environment with `conda create --name cellpose python=3.9`. We recommend python 3.9, but python 3.10 will likely work as well.
 4. To activate this new environment, run `conda activate cellpose`
 5. (option 1) To install cellpose with the GUI, run `python -m pip install cellpose[gui]`.  If you're on a zsh server, you may need to use ' ': `python -m pip install 'cellpose[gui]'`.
 6. (option 2) To install cellpose without the GUI, run `python -m pip install cellpose`. 

cellpose/__main__.py

@@ -155,16 +155,26 @@ def main():
                 builtin_size = False
                 if args.all_channels:
                     channels = None
+                    img = io.imread(image_names[0])
+                    if img.ndim == 3:
+                        nchan = min(img.shape)
+                    elif img.ndim == 2:
+                        nchan = 1
+                    channels = None
+                else:
+                    nchan = 2
+
                 pretrained_model = None if model_type is not None else pretrained_model
                 if restore_type is None:
                     model = models.CellposeModel(gpu=gpu, device=device,
                                                  pretrained_model=pretrained_model,
                                                  model_type=model_type,
+                                                 nchan=nchan,
                                                  backbone=backbone)
                 else:
                     model = denoise.CellposeDenoiseModel(
                         gpu=gpu, device=device, pretrained_model=pretrained_model,
-                        model_type=model_type, restore_type=restore_type,
+                        model_type=model_type, restore_type=restore_type, nchan=nchan,
                         chan2_restore=args.chan2_restore)
 
             # handle diameters

docs/installation.rst

@@ -31,7 +31,7 @@ this code at the beginning of your notebook before you import cellpose:
 M1 Mac installation
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-Please use the instructions provided on `image.sc <https://forum.image.sc/t/cellpose-on-macos-m1-pro-apple-silicon-arm64/68018/4>` 
+Please use the instructions provided on `image.sc <https://forum.image.sc/t/cellpose-on-macos-m1-pro-apple-silicon-arm64/68018/4>`_ 
 by Peter Sobolewski. From the command line you can choose the Mac device with
 
 ::