Bioimage Analysis Workshop Taipei

Course material for bioimage analysis workshop at Academia Sinica, Taipei. The course materials are heavily based on:

• 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

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” work flow as below for the setup.
• If you are not confortable with python, please follow the “Basics in Python” Jupyter notebook to learn the basics of python programming
• If you want something more to get yourself more comfortable with python programming for image proessing, follow “Basics in Python2” Jupyter notebook. (to be updated)

Creating a Python Environment for the workshop

1. With 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
   conda install matplotlib
   conda install scipy
   conda install scikit-image
   conda install ipywidgets
   
   jupyter nbextension enable --py --sys-prefix widgetsnbextension

4. In anaconda navigator, change the environment to the newly created environment

   

5. Install Jupyter notebook in this environment

6. Launch the jupyter notebook