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fix denoise display, install instruction
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active_plugins/runcellpose.py

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@@ -1048,7 +1048,7 @@ def display(self, workspace, figure):
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colormap="gray",
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image=workspace.display_data.denoised_image,
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sharexy=figure.subplot(0, 0),
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title=self.denoise.value,
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title=self.denoise_name.value,
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x=2,
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y=1,
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)

documentation/CP-plugins-documentation/runcellpose.md

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@@ -36,11 +36,16 @@ python -m pip install --force-reinstall -v cellpose==2.3.2
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### Cellpose 3
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In a Python 3.9 environment that has Cellprofiler installed, run the following commands to install Cellpose 3:
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On Mac M1/M2, to create a new environment with CellProfiler and Cellpose 4, run the following commands:
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```bash
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python3.9 -m pip install cellpose==3.1.1.2
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python3.9 -m pip install numpy==1.24.4
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export LDFLAGS="-L/opt/homebrew/opt/mysql@8.0/lib"
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export CPPFLAGS="-I/opt/homebrew/opt/mysql@8.0/include"
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export PKG_CONFIG_PATH="/opt/homebrew/opt/mysql@8.0/lib/pkgconfig"
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conda create -y --force -n cellpose3_cellprofiler python=3.9 h5py=3.6.0 python.app scikit-learn==0.24.2 scikit-image==0.18.3 openjdk
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conda activate cellpose3_cellprofiler
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pip install cellpose==3.1.1.2
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pip install mysqlclient==1.4.6 cellprofiler
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```
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### Cellpose-SAM (Cellpose 4)

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