@@ -54,31 +54,33 @@ The following assumes that you have installed python using Mambaforge as [descri
...
@@ -54,31 +54,33 @@ The following assumes that you have installed python using Mambaforge as [descri
-**Linux**: Open your terminal application
-**Linux**: Open your terminal application
2.We use an environment to encapsulate the python tools used for this workshop. This ensures that the requirements for this workshop do not interfere with your other python projects. To create the environment (named `pyimagecourse`), enter the following command.
2.Navigate to the `notebooks` subdirectory of the `bioimage_analysis_with_python_course` directory you downloaded.
```bash
```bash
mamba create -n pyimagecourse python=3.10
cd <path to bioimage_analysis_with_python_course>/notebooks
```
```
3. Once the environment setup has finished, activate the environment. If you successfully activated the environment, you should now see `(pyimagecourse)` to the left of your command prompt.
3. The file `environment.yml` contains the dependencies needed to run the notebooks, and it specifies a `conda` environment named `pyimagecourse`. Create this environment from the file by entering the following command.
```bash
```bash
mamba activate pyimagecourse
mamba create --file environment.yml
```
```
4.Install the dependencies with the commands below
4.Once the environment setup has finished, activate the environment. If you successfully activated the environment, you should now see `(pyimagecourse)` to the left of your command prompt.
6. Test that your notebook installation is working. We will be using notebook for interactive analysis. Enter the command below and it should launch jupyter notebook book in a web browser.
5. Test that your notebook installation is working. We will be using notebook for interactive analysis. Enter the command below and it should launch jupyter notebook book in a web browser.
```bash
```bash
jupyter notebook
jupyter notebook
```
```
7. Test your napari installation. Enter the command below and an empty napari viewer should open. You can close the window after it opens. Please note that it takes a bit of extra time to launch napari the first time.
6. Test your napari installation. Enter the command below and an empty napari viewer should open. You can close the window after it opens. Please note that it takes a bit of extra time to launch napari the first time.
