First week

1. Before the first class:

Watch the video here: https://www.ibiology.org/talks/light-microscopy/
Download Zotero and setup a free account. We will use this software to organize articles and references.
- Email me as soon as you create an account and let me know what your username is. I will then add you to the class shared repository.

2. On the first day of class, Tuesday 1/29

10:45 - 12:05: Go through Tutorial 1. This introduces you to ImageJ and Python. Do this work individually though you may get help from your classmates. To complete this tutorial you will need Fiji and Python (version 2.7). The computers in 291 should all have both of these software packages installed. But they are both also free and you may download and install on any computer. The images you need for that are here (for Part 1) and here (for Part 2). Download both to the computer you will be using.
2:30 - 5:20: Go through Tutorial 2. This goes over making samples and using the microscopes in 292. You will also be collecting data to be analyzed on Thursday. Do this work in your lab group pairs (however, you must each turn in the requested answers/plots). You will either be using the Olympus microscope or the Optical Tweezers assembly (but just in microscope-mode, not tweezers-mode). In both cases, make sure you are using a 40x, air objective. Ask someone for assistance if you aren't sure what to do.
You should complete Tutorials 1 and 2 by the end of Tuesday.

3. Before the second class, do the following so you'll be prepared to use Python for data analysis:

Read through the introductory chapter to the textbook A Student's Guide to Python for Physical Modeling which can be found here.
Go completely and carefully through this Python tutorial which can be opened using Jupyter notebook. Instructions for using Jupyter notebook can be found here. There is also plenty of documentation to be found online.
Get familiar with what Github is. For Thursday's tutorial you will need to pull code from a Github repository.

4. On the second day of class, Thursday 1/31

10:45 - 12:05: Go through Tutorial 3. For this you will need to use the videos acquired of diffusing beads from Tuesday. You will analyze this using Python with the Jupyter notebook platform.