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

  1. Install Fiji on your machine, as described here.
  2. Add the following updates sites, as described here.
    • IJPB-Plugins

ImageJ Macro

Install Fiji

  1. Install Fiji on your machine, as described here.
  2. Add the following updates sites, as described here.
    • IJPB-Plugins

ImageJ Jython

Install Fiji

  1. Install Fiji on your machine, as described here.
  2. Add the following updates sites, as described here.
    • IJPB-Plugins

skimage napari

Install skimage napari

Essentially, follow these instructions: https://alisterburt.github.io/napari-workshops/SciPy-0722/scipy_installation.html

Installation (only once)

  1. install miniconda (TODO)
  2. conda create -n skimage-napari-tutorial python=3.9
  3. conda activate skimage-napari-tutorial
  4. conda install -c conda-forge notebook matplotlib
  5. pip install aicsimageio
  6. conda install -c conda-forge openjdk=11.0.8
  7. conda install -c conda-forge bioformats_jar
  8. pip install "napari[all]"
  9. pip install napari-brightness-contrast
  10. pip install napari-plot-profile
  11. create a directory called skimage-napari-tutorial (e.g. on your Desktop)
  12. download load_from_url.py
  13. move load_from_url.py in skimage-napari-tutorial directory

Test installation (only once)

  1. conda activate skimage-napari-tutorial
  2. jupyter notebook
  3. napari

Start (every time)

  1. open a terminal
  2. go to skimage-napari-tutorial
  3. conda activate skimage-napari-tutorial
  4. 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: