Bioimage-Analysis-Workshop-23-24

The course materials for the bioimage analysis workshop at LiMe, KyotoU. Please note that these materials have been heavily adopted from:

• EMBL Bio-IT bioimage analysis workshop, especially the part by Toby Hodges and Jonas Hartmann: https://git.embl.de/grp-bio-it-workshops/image-analysis-with-python
• Introduction to Bioimage Analysis by Pete Bankhead: https://bioimagebook.github.io/
• Bioimage Analysis Lecture 2020 by Robert Haase: https://www.youtube.com/watch?v=e-2DbkUwKk4&list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U
• Bioimaging Guide by Various People: https://www.bioimagingguide.org/

Pre-requirement of the workshop

Please prepare the following before the workshop:

• Please install Anaconda (https://www.anaconda.com/) on your laptop (Yes, you need a laptop) and follow the “Creating a Python Environment for the workshop” workflow below for the setup.

Creating a Python Environment for the workshop

1. With the Anaconda prompt, create a virtual environment with the name “bioimage-analysis”

   conda create --name bioimage-analysis python=3.8

2. Then activate the environment

   conda activate bioimage-analysis

3. Install all the necessary packages

   conda install numpy matplotlib scipy scikit-image ipywidgets jupyter jupyterlab 

   then install Napari with

   python -m pip install "napari[all]"

4. Launch the Jupyter Lab by

   jupyter lab

5. Navigate to the downloaded files