Imaging and Spectral Data Analysis in Python

We present a set of jupyter notebooks and presentations that go over the basics of:

• Image and spectral data analysis in Python
• USID, pyUSID, and pycroscopy as tools for analyzing large and multidimensional imaging / spectroscopy datasets

This material was developed as part of the 2018 CNMS User Meeting

See our list of tutorials for more information

Getting started

(Recommended) Working on your personal computer

1. (one time only) Install necessary software:
   1. Follow these instructions to install Anaconda + pycroscopy on your own laptop
   2. Also please install pyUSID via: pip install pyUSID just like how you installed pycroscopy
2. (one time only) Download the contents of this tutorial onto your computer:
   1. click on the green Clone or download button
   2. Click on Download ZIP
   3. Download the zip file to your Documents / Downloads / Desktop
   4. Unzip the zip file
3. Start up a Jupyter Notebook:
   1. Start a terminal:
      1. Windows users: Click on Start >> Anaconda3 >> Anaconda Prompt
      2. Mac / Linux users: Open Terminal. You can find it by holding down your Command and Space key and typing Terminal in the search bar that pops up.
   2. In the Terminal or Anaconda Prompt, type jupyter notebook and press the Enter or Return key. If everything happened correctly, a new tab should pop up on your default browser showing familiar folders such as Desktop, Documents, etc.
   3. Do not close the Terminal or Anaconda Prompt!
4. Finally, work on the notebooks in this tutorial:
   1. Navigate to the folder (e.g. - Desktop) where you unzipped the zip file in step 2.
   2. Click on the index.ipynb file which should present a new tab on your browser that looks like this
5. Once you are done working on the jupyter notebooks:
   1. Go back to the Terminal or Anaconda Prompt. Hold down the Ctrl (control) key and press the C key twice to shut down the Jupyter server.
   2. You can now close the Jupyter browser tabs and the Terminal or Anaconda Prompt

We understand that this may seem a little tedious in the beginning but we assure you that you will get used to this very quickly

Trying out the tutorial online

If you are having trouble with installing Anaconda on your personal computer (above), please try one of the following:

• Azure notebooks

  1. You will need to sign up for a Microsoft (Outlook, Hotmail, ...) account if you don't already have one.
  2. Once you are logged in, click here
  3. Next, click on the Clone button (just above the search bar) to make your own copy of the project
  4. Once your copy of the project has been created, click on the Run button along the same line as the Clone button
  5. You should be directed to a familiar Jupyter notebook server page.

• Binder

  • The benefit of Binder is that one does not need a Microsoft account, but the drawback is that your solutions / edits will be lost if you close the browser tab(s)
  • Click here to launch the jupyter notebook server. This will take a while so please be patient.

Finally, for either option, click here to get started with the notebooks

Getting help

Please get in touch with us on our Google group