Add fish.png, remove imaging workshop pdf

Author: MalloryWittwer

content/python-intro/Content.ipynb

@@ -17,98 +17,6 @@
     "\n",
     "This notebook introduces the basics of image handling and manipulation in Python, using <a href=\"https://scikit-image.org/\">Scikit-image</a>, <a href=\"https://matplotlib.org/stable/\">Matplotlib</a>, and <a href=\"https://numpy.org/\">Numpy</a>.\n",
     "\n",
-    "➡️ <a href=\"https://github.com/EPFL-Center-for-Imaging/ImagingLunch_ImagesInPython\">Git repository</a>."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "01e44911",
-   "metadata": {
-    "editable": true,
-    "slideshow": {
-     "slide_type": "subslide"
-    },
-    "tags": []
-   },
-   "source": [
-    "```{admonition} How to use this notebook?\n",
-    "This document is an interactive <a href=\"https://jupyter.org/\">Jupyter notebook</a>. Use `Shift`+`Enter` to run individual code cells.\n",
-    "```"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "6507408c",
-   "metadata": {
-    "editable": true,
-    "slideshow": {
-     "slide_type": "fragment"
-    },
-    "tags": []
-   },
-   "source": [
-    "## Why use Python for image analysis?\n",
-    "\n",
-    "- ✅ Easy to learn and use\n",
-    "- ✅ Free & open-source\n",
-    "- ✅ Wide range of libraries\n",
-    "- ✅ Implement custom functions & tools\n",
-    "- ✅ Automate image analysis via scripts\n",
-    "- ✅ Deep learning & data science\n",
-    "- ✅ Explore data in Juptyer notebooks"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "4a377b85",
-   "metadata": {
-    "editable": true,
-    "slideshow": {
-     "slide_type": "subslide"
-    },
-    "tags": []
-   },
-   "source": [
-    "## Contents\n",
-    "\n",
-    "We'll cover the following topics:\n",
-    "\n",
-    "- <a href=\"#opening-our-first-image\">Opening our first image</a>\n",
-    "- <a href=\"#how-are-digital-images-represented-in-python\">How are digital images represented in Python?</a>\n",
-    "- <a href=\"#selecting-and-modifying-pixel-values\">Selecting and modifying pixel values</a>\n",
-    "- <a href=\"#opening-images-from-files\">Opening images from files</a>\n",
-    "- <a href=\"#applying-image-processing-filters\">Applying image processing filters</a>\n",
-    "- <a href=\"#thresholding\">Thresholding</a>\n",
-    "- <a href=\"#analyzing-individual-objects\">Analyzing individual objects</a>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "048880e7",
-   "metadata": {},
-   "source": [
-    "## Packages\n",
-    "\n",
-    "We'll use the packages listed in the requirements file (<a href=\"./requirements.txt\">requirements.txt</a>). To make sure you have installed these packages, you can run the Jupyter \"magic\" command below:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2c396e26",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%pip install -qr requirements.txt"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "fea92a32",
-   "metadata": {},
-   "source": [
-    "## Imports\n",
-    "\n",
     "We start by importing the `data` module from <a href=\"https://scikit-image.org/\">Scikit-image</a>, which provides example images, and Matplotlib's `pyplot` module which we'll use to display images."
    ]
   },
@@ -435,8 +343,8 @@
    "source": [
     "import skimage.io\n",
     "\n",
-    "# Image source: VIATICALPES (https://catima.unil.ch/viatimages/en)\n",
-    "image = skimage.io.imread(\"limmat_fish.tif\")\n",
+    "# Image source https://catima.unil.ch/viatimages\n",
+    "image = skimage.io.imread(\"fish.png\")\n",
     "\n",
     "plt.imshow(image);\n",
     "\n",

content/python-intro/Intro_Python_Lunch.pdf

@@ -1,7 +1,8 @@
-# numpy
-# pandas
-# matplotlib
-# jupyterlab
-# scikit-image
+numpy
+pandas
+matplotlib
+jupyterlab
+scikit-image
 tifffile
+jupyterlab
 jupyterlab-myst