Course preparation#

Before attending the course, please install conda on your computer as explained in this blog post. Furthermore, please install devbio-napari and Github desktop.

When you are done, you can test your setup by executing these commands from the command line:

conda activate devbio-napari-env

naparia

After Napari opens, click the menu File > Open Samples > clEsperanto > blobs (from ImageJ). In the Panel on the right click on the Label button. If Napari then looks like this, you are ready to go:

img.png

Troubleshooting: Errors in Jupyter lab#

In case you installed devbio-napari between approximately December 6st and December 11th, there are error messages appearing in Jupyter lab such as those shown below (potentially related to this).

This can be fixed by calling this from inside the devbio-napari-env environment:

mamba install jupyter_server=1.23.3 -c conda-forge

Troubleshooting: Napari jumping out of the screen#

When using some plugins, the Napari window increases and jumps out of the screen. In this case, downgrade Napari to version 0.4.15:

mamba install napari=0.4.15 -c conda-forge

Troubleshooting: DLL load failed#

In case of error messages such as this one:

[...] _get_win_folder_with_pywin32
from win32com.shell import shellcon, shell
ImportError: DLL load failed while importing shell: The specified procedure could not be found.

Try this command, within the base environment:

conda activate base

pip install --upgrade pywin32==228

Source

Troubleshooting: Graphics cards drivers#

In case error messages contains “ImportError: DLL load failed while importing cl: The specified procedure could not be found” see also or “”clGetPlatformIDs failed: PLATFORM_NOT_FOUND_KHR”, please install recent drivers for your graphics card and/or OpenCL device. Select the right driver source depending on your hardware from this list:

Sometimes, mac-users need to install this:

mamba install -c conda-forge ocl_icd_wrapper_apple

Sometimes, linux users need to install this:

mamba install -c conda-forge ocl-icd-system

In case installation didn’t work in the first attempt, you may have to call this command line to reset the napari configuration:

napari --reset