Workshop on python basics and its application to biological image or video analysis

Summer, 2018

Wednesday, 2:30 PM - 4:00 PM

Introduction to python and its powerful packages for image and video processing, data analysis, visualization, machine learning and parallel computation.

Walk through python codes of sample image/video bioinformatic projects.

Make you fall in love with Python!

1. Experimental methods in systems biology: Coursera Links
2. Cellular and molecular biology techniques:WIKI JoVE
3. High-throughput Microscopy: Jan Ellenberg's lecture
4. Axio Zeiss Microscope tutorial: video links
5. TIMING 2 project: project links

1. Introduction to Python, Anaconda, Spyder and basic python syntax.

   a. Python Official Site links

   b. Anaconda Download, 11 mins video tutorial

   c. Basic Python Syntax Links

   d. Visualize python code step by step PythonTutor

2. Common Python packages: os, system, numpy and scipy.

   a. os package link, pay attention to: os.listdir, os.mkdir, os.system;

   b. sys package link, pay attention to: sys.argv;

   c. numpy package link;

   d. scipy package link;

3. Efficient image processing with Python: scikit-image, opencv or SimpleITK? slides, code

4. Manage your data in standard format with Python: PANDAS slides ipynb iris.csv

5. User-friendly Graphical User Interface(GUI): PyQt slides, demo

6. Machine Learning with Python: scikit-learn slides

7. Data Visaulization with Python: matplotlib, seaborn and yellowbrick slides

8. Deep Learning with Python: tensorflow and Keras slides

9. Multi-threading with Python: multiprocessing slides

10. Design of TIMING-pipeline and TIMING-viewer slides

11. Useful Links Python Programming.