Tool installation
Learning Objectives
After completing this lesson, learners should be able to:
Install the software that is required to execute the activities in this training material
Motivation
Provide instructions for installing the software required for this workshop. Please follow the instructions given by your trainer regarding which software you will need!
Concept map
graph TD
I("Image Analysis") -->|with| C("Computer")
C -->|using| T("Tools")
T -->|require| S("Installation")
Figure

Installation instructions
To visualise the installation instructions, please select the required platform in the activity list.
Show activity for:
ImageJ GUI
Install Fiji
ImageJ Macro
Install Fiji
ImageJ Jython
Install Fiji
skimage napari
Install skimage napari
Essentially, follow these instructions: https://alisterburt.github.io/napari-workshops/SciPy-0722/scipy_installation.html
Installation (only once)
- install miniconda (TODO)
conda create -n skimage-napari-tutorial python=3.9
conda activate skimage-napari-tutorial
conda install -c conda-forge notebook matplotlib
pip install aicsimageio
conda install -c conda-forge openjdk=11.0.8
conda install -c conda-forge bioformats_jar
pip install "napari[all]"
pip install napari-brightness-contrast
pip install napari-plot-profile
- create a directory called
skimage-napari-tutorial
(e.g. on your Desktop)- download load_from_url.py
- move
load_from_url.py
inskimage-napari-tutorial
directoryTest installation (only once)
conda activate skimage-napari-tutorial
jupyter notebook
napari
Start (every time)
- open a terminal
- go to
skimage-napari-tutorial
conda activate skimage-napari-tutorial
jupyter notebook
New > Python 3
MATLAB
Install MATLAB or GNU Octave
- MATLAB is a licensed software by MathWorks. Please contact your Institution to verify if you have access to a license. If this is the case, you can find detailed instructions on how to install the software here.
- Alternatively, GNU Octave is a free and open-source alternative to MATLAB which shares its syntax (more about compatibility at this link). Installation instructions can be found here.
Follow-up material
Recommended follow-up modules:
Learn more: