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<script>DOCUMENTATION_OPTIONS.pagename = '00_python/00_python_intro';</script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Introduction to Python in Jupyter Notebook/Google Colab" href="01_Python_Basics.html" />
<link rel="next" title="Python" href="00_Python_prez.html" />
<link rel="prev" title="Welcome to MB100T01 Course" href="../intro.html" />
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="current nav bd-sidenav">
<li class="toctree-l1 current active has-children"><a class="current reference internal" href="#">Brief introduction to Python</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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</div>
</a>
<a class="right-next"
href="01_Python_Basics.html"
href="00_Python_prez.html"
title="next page">
<div class="prev-next-info">
<p class="prev-next-subtitle">next</p>
<p class="prev-next-title">Introduction to Python in Jupyter Notebook/Google Colab</p>
<p class="prev-next-title">Python</p>
</div>
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<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Working with tabular data and Statistics" href="../01_pandas_statistics/intro.html" />
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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="current nav bd-sidenav">
<li class="toctree-l1 current active has-children"><a class="reference internal" href="00_python_intro.html">Brief introduction to Python</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="00_Python_prez.html">Python</a></li>
<li class="toctree-l2 current active"><a class="current reference internal" href="#">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<div class="prev-next-area">
<a class="left-prev"
href="00_python_intro.html"
href="00_Python_prez.html"
title="previous page">
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<p class="prev-next-subtitle">previous</p>
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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<li><p>statannotations (for adding statistical test results to plots)</p></li>
<li><p>scikit_posthocs (for post-tests)</p></li>
</ul>
<p>Open a terminal, activate the environment and install the necessary additional packages by running the commands below:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mamba</span> <span class="n">activate</span> <span class="n">devbio</span><span class="o">-</span><span class="n">napari</span><span class="o">-</span><span class="n">env</span>

<span class="n">pip</span> <span class="n">install</span> <span class="n">scikit_posthocs</span> <span class="n">statannotations</span> <span class="n">watermark</span> <span class="n">pivottablejs</span> <span class="n">seaborn</span><span class="o">==</span><span class="mf">0.12.2</span>
</pre></div>
</div>
<p>We will use these two presentations:</p>
<ul class="simple">
<li><p><a class="reference download internal" download="" href="../_downloads/0d731dfb94b83dbd30f3c3a684ee5d19/Tabular_Data.pdf"><span class="xref download myst">Tabular_Data</span></a></p></li>
<li><p><a class="reference download internal" download="" href="../_downloads/13ced125cda365f10e753d9efb06458d/Statistics.pdf"><span class="xref download myst">Statistics</span></a></p></li>
</ul>
<div class="toctree-wrapper compound">
</div>
</section>
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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="../00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="../00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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<p>This part will teach you how to plot data with matplotlib and seaborn. We start with matplotlib, because seaborn is based upon it and some syntax may be useful with seaborn.</p>
<p>We then look at sophisticated and stylish plots straight from pandas dataframes. You will learn how to plot scatter plots, boxplots, distribution plots and even multivariate plots. We also show how to add statistical annotations to your plots as a convenient way to display statistical test results on the figures.</p>
<p>Finally, you will employ all the tools learned during the previous sections to work on a complete image analysis workflow, from reading raw images, through image processing and feature extraction, to displaying your data analysis results in figures.</p>
<p>We will use these two presentations:</p>
<ul class="simple">
<li><p>[Preparing Visuals of Data Analysis DV](./Preparing Visuals of Data Analysis DV.pdf)</p></li>
<li><p><a class="reference download internal" download="" href="../_downloads/1a27f61c8a10e7f1e0479acc21027ad2/Plotting.pdf"><span class="xref download myst">Plotting</span></a></p></li>
</ul>
<div class="toctree-wrapper compound">
</div>
</section>
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# Python

This section focuses on introduction to Python. Python is a versatile and beginner-friendly programming language widely used in various fields, including computer science, data science, web development, and artificial intelligence.

## Key Points

1. **Readable and Easy to Learn:**
- Python is designed for simplicity and readability, making it easy for beginners to understand.

2. **Interpreted Language:**
- Python is interpreted, allowing you to run code without a separate compilation step, making development faster and more interactive.

3. **General-Purpose:**
- Python is a general-purpose language suitable for diverse applications, from web development to scripting.

4. **Extensive Standard Library:**
- Python comes with a rich standard library, reducing the need for writing code from scratch for common tasks.

5. **Community Support:**
- A large and active community provides resources, tutorials, and forums for support and collaboration.

6. **Object-Oriented Programming:**
- Python supports object-oriented programming, organizing code in a modular way.

7. **Versatility in Application:**
- Used in web development (Django, Flask), data science (NumPy, TensorFlow), and more, making it versatile for different career paths.

8. **Cross-Platform Compatibility:**
- Compatible with major operating systems (Windows, macOS, Linux), ensuring code can run on different platforms without modification.

## Conclusion

In summary, Python is a beginner-friendly, versatile, and powerful programming language, providing a solid foundation for learning how to program. Its simplicity, readability, and extensive community support make it an excellent choice for beginners.


We will use these presentations:
* [Python_basics](./Python_basics.pdf)
* [Python_algorithms](./Python_algorithms.pdf)
* [Short - KONFMI_prez_Python](./KONFMI_prez_Python.pdf)
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* statannotations (for adding statistical test results to plots)
* scikit_posthocs (for post-tests)

Open a terminal, activate the environment and install the necessary additional packages by running the commands below:

```
mamba activate devbio-napari-env
pip install scikit_posthocs statannotations watermark pivottablejs seaborn==0.12.2
```
We will use these two presentations:
* [Tabular_Data](./Tabular_Data.pdf)
* [Statistics](./Statistics.pdf)
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We then look at sophisticated and stylish plots straight from pandas dataframes. You will learn how to plot scatter plots, boxplots, distribution plots and even multivariate plots. We also show how to add statistical annotations to your plots as a convenient way to display statistical test results on the figures.

Finally, you will employ all the tools learned during the previous sections to work on a complete image analysis workflow, from reading raw images, through image processing and feature extraction, to displaying your data analysis results in figures.

We will use these two presentations:
* [Preparing Visuals of Data Analysis DV](./Preparing Visuals of Data Analysis DV.pdf)
* [Plotting](./Plotting.pdf)
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<p aria-level="2" class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="00_python/00_python_intro.html">Brief introduction to Python</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2"><a class="reference internal" href="00_python/00_Python_prez.html">Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="00_python/01_Python_Basics.html">Introduction to Python in Jupyter Notebook/Google Colab</a></li>


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