Lab Course for Biotechnology Master Students

Methods in Cell Analysis and Laboratory Automation (Fall 2024)

Image Analysis Fundamentals

In preparation for the course:

Download and extract the complete course material → iaf/
Install Python following the instructions in iaf/Python.pdf, chapter 1.2.
Create the `iaf-env` conda environment following the instructions in iaf/Python.pdf, chapter 1.4.

Please note: the zip file contains all needed material (with the exception of the homework). However, individual files can also be downloaded from the links below.

First day: Theoretical session (Room: BSS E 23)

Quick and partial theoretical introduction to the main concepts of the course.
Course text: iaf/Theory.pdf.
Couse slides: iaf/Theory_slides.pdf.

Second day: Practical session /I (Room: BSS E 23)

Introduction to Python and the basics of Image Processing in Python.

Course text: iaf/Python.pdf, chapters 2 - 6.
Code: iaf/code/python.

Analysis of data from a (fictitious) drug discovery study (part I: image processing).

Assignment: iaf/Analysis_Hands_On.pdf.
Dataset: iaf/data/hands-on/plate01.zip.

Third day: Practical session /II (Room: BSS E 23)

Introduction to simple data analysis.

Course text: iaf/Python.pdf, chapters 7.

Analysis of data from a (fictitious) drug discovery study (part II: data analysis).

Assignment: iaf/Analysis_Hands_On.pdf.
Dataset: your results from the previous day.

Homework

To successfully complete the Image Analysis Fundamentals course, you must solve and submit this homework for review.
In the assignment (section "Your submission"), you can find all information on submission deadline and how to upload your solution. Have fun!

Recommended reading

University of Alabama at Birmingham: Good practices in scientific image processing and analysis.
iaf/Good_Practices.pdf: A summary of the most important points.

Optional

For those courageous enough, we offer a test environment for the course on our Reproducible Research Platform: https://rrp-tst.ethz.ch.

How to use:

Log in with your ETH credentials.
Click on the button next to "Your projects" on the top left corner of the page.
Click on Share identifier in the "Create new project from" menu.
In the Project section, paste this identifier in the "Source" field: N2ZhZWU5ZWEtM2E4Yi00OGJlLWJjNGQtMmIwYzhjNzIzNTgzIGN1bnlhIHI2ZHE1aiBveHRzdThnMQ==
Under Resources, set "Memory in Gb" to 3.0 and "Number of CPUs" to 0.2. Make sure to press the Enter key after every change!
Click on the button to build the environment.
When the environment is ready, click on the to start it.