https://github.com/pycroscopy/cnms_um_2018_spima

Introduction to Spectral and Image processing in Python
https://github.com/pycroscopy/cnms_um_2018_spima

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Introduction to Spectral and Image processing in Python

• Host: GitHub
• URL: https://github.com/pycroscopy/cnms_um_2018_spima
• Owner: pycroscopy
• License: mit
• Created: 2018-07-09T12:13:02.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2019-08-09T18:47:26.000Z (almost 7 years ago)
• Last Synced: 2025-03-25T16:22:54.477Z (about 1 year ago)
• Topics: notebooks
• Language: Jupyter Notebook
• Homepage:
• Size: 81.8 MB
• Stars: 6
• Watchers: 6
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
# 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](https://pycroscopy.github.io/pyUSID/data_format.html), [pyUSID](https://pycroscopy.github.io/pyUSID/about.html), 

  and [pycroscopy](https://pycroscopy.github.io/pycroscopy/about.html) as tools for analyzing large and multidimensional imaging / spectroscopy datasets 

    

This material was developed as part of the [2018 CNMS User Meeting](./CNMS_UM_Workshop_schedule.md)

See our [list of tutorials](https://pycroscopy.github.io/pyUSID/external_guides.html) for more information

  

## Getting started

### (Recommended) Working on your personal computer

1. (one time only) Install necessary software:

    1. Follow [these instructions](https://pycroscopy.github.io/pycroscopy/install.html) 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](./index.ipynb)

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](https://signup.live.com/?wa=wsignin1.0&rpsnv=13&ct=1533149109&rver=6.7.6643.0&wp=MBI_SSL&wreply=https%3a%2f%2faccount.microsoft.com%2fauth%2fcomplete-signin%3fru%3dhttps%253A%252F%252Faccount.microsoft.com%252F%253Frefd%253Daccount.microsoft.com%2526refp%253Dsignedout-index&id=292666&lw=1&fl=easi2&pcexp=true&uictx=me&contextid=D0A988B000A50828&bk=1533149128&uiflavor=web&uaid=098dd33703314790a45fcfb799fd93d3&mkt=EN-US&lc=1033&lic=1) for a Microsoft (Outlook, Hotmail, ...) account if you don't already have one.

    2. Once you are logged in, click [here](https://notebooks.azure.com/ssomnath/libraries/cnms2018um)

    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](https://mybinder.org/v2/gh/pycroscopy/pyUSID_Tutorial/master) to launch the jupyter notebook server.

      This will take a while so please be patient.

      

Finally, for either option, click [here](./index.ipynb) to get started with the notebooks

## Getting help

Please get in touch with us on our [Google group](https://groups.google.com/forum/#!forum/pycroscopy)