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Update installation instructions #2

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Oct 21, 2024
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Update installation instructions #2

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25 changes: 17 additions & 8 deletions workshop/0_workshop_preparation/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,18 +14,27 @@ We will require `Mamba` for installing and managing python environement and pack
> [!CAUTION]
> `Conda` should also work but will be slower for downloading and installing the dependencies

### DevBio environment
### devbio-napari environment

Using mamba, please install the [devbio-napari]() package into a fresh enviroment, e.g. using this command:
Using mamba, please install the [devbio-napari](https://github.com/haesleinhuepf/devbio-napari) package into a fresh enviroment, e.g. using this command:

```bash
mamba create --name devbio python=3.11 devbio-napari pyqt -c conda-forge -y
```

When the installation is done, you can activate the environment and test that all was correctly install by running the following command:
Afterwards, please use pip to get the most recent version (which is not available via conda-forge yet):
```bash
pip install devbio-napari==0.11.0
```

When the installation is done, you can activate the environment...
```bash
mamba activate devbio
```
... and start Napari with the Assistant interface:

```bash
mamba activate devbio && naparia
naparia
```

Napari should start with the pyclesperanto-assistant:
Expand All @@ -34,9 +43,9 @@ Napari should start with the pyclesperanto-assistant:

### Troubleshouting

Any issues will be gladly answered during the workshop, do not hesite to comeforth.

If the user interface does not look like shown above, e.g. has much less buttons, you may need to install additional packages or GPU drivers. Read this [troubleshooting section](https://github.com/clesperanto/pyclesperanto?tab=readme-ov-file#troubleshooting-graphics-cards-drivers) for more details.

Any additional issues will be gladly answered during the workshop, do not hesite to comeforth.

## Fiji

Expand All @@ -47,7 +56,7 @@ clesperanto is also being developed in FIJI. Although no proper release is avail
Start the update of your FIJI and when it is done, go to the update site list
- `Help menu > Update` then click on `Manage update sites`
- Click on `add unlisted site`
- Add the following site ``
- Add the following site `https://sites.imagej.net/clij3`
- Validate the changes and restart FIJI

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