Setting up your computer

Setting up your computer#

This chapter provides instructions for setting up your computer to run Python to analyse images.

Setting up Python and Conda environments#

When working with Python, we will make use of many plugins and software libraries which need to be organized. One way of doing this, is by managing Conda environments. A conda environment can be seen as a virtual desktop, or virtual computer, accessible via the terminal. If you install some software into one Conda environment, it may not be accessible from another environment. If a Conda environment breaks, e.g. incompatible software was installed, you can just make a new one and start over.

Step 1: Install Mambaforge#

Download and install Conda. We recommend the Conda distribution Mambaforge.

For ease-of-use, it is recommended to install it for your use only and to add Conda to the PATH variable during installation.

Step 2: Install devbio-napari#

We recommend installing devbio-napari, a distribution of napari with a set of plugins for bioimage analysis.

Use this command from the terminal:

mamba create --name devbio-napari-env python=3.9 devbio-napari -c conda-forge

Tip: It is recommended to create one environment for every project you are executing. In that way installed software libraries and tools cannot harm each other.

Step 3: Testing the installation#

Afterwards you can enter the environment to work with it. Whenever you want to work on the same project again, you should start a command line and enter this:

mamba activate devbio-napari-env

Start Jupyter lab from the terminal like this

jupyter lab

A browser will open and show you the following web page. In the sectiojn Notebook click on “Python 3 (ipykernel)” to create a new notebook:

In the new notebook, click in the first code cell, enter print("Hello world") and hit SHIFT+ENTER on your keyboard. If everything is installed properly, it should look like this:

To test if your graphics card driver is properly installed, enter this code:

import pyclesperanto_prototype as cle

cle.get_device()

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

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