Tutorial 1: Using Python and ImageJ

Before you can begin the tasks enumerated below, you'll need Python. The computers in 292 should have Python installed. Specifically, they should have the Python collection Anaconda installed. I encourage you to download and install that on your own personal computer too. If you do so, make sure you download the Python 2.7 version.

How will you interface with Python? A couple options. One is to use Spyder. The other is using Jupyter Notebook. Note that both are packaged with the Anaconda installation. So you don't need to download and install these programs separately.

You may have questions or run into problems. If you're unsure about how to get started, just let me know (in particular, running the Jupyter notebooks (those *.ipynb files) can be kind of tricky -- though the documentation is here -- so just come by my office and I can walk you through it).

Note that you don't have to do these tasks in the order listed.

You only need to turn in what is indicated in the instructions for item #3.

1. Read over the first chapter of A Student’s Guide to Python for Physical Modeling (the Introduction) which you can find as a pdf on the site linked to.
2. Go through a couple Python tutorials created by others (and you are encouraged to seek out more such tutorials -- they're easy to find and a great way to learn programming).
   • Step through the "00-python-intro.ipynb" Notebook (see the attachments below).
   • Check out the Python/Numpy tutorial here: https://github.com/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/02.02-The-Basics-Of-NumPy-Arrays.ipynb.
   • You can download that notebook by right-clicking "Raw" and selecting "Save As." Then use Jupyter Notebook to open and run.
3. Second, go through the ImageJ/Python 381 tutorial. You'll find the pdf document with the step-by-step instructions attached below.
   • As part of this, you should watch the video here.
   • And you'll need the program Fiji (which stands for Fiji Is Just ImageJ). Note that I'll use the words Fiji and ImageJ to mean the same thing.
   • You'll also need image files to use in this tutorial. Find those images here.
4. Finally, read: Thorn, K. A quick guide to light microscopy in cell biology. Mol. Biol. Cell 27, 219–222 (2016). The article can be found on Zotero or here.

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