{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 5. Filtering exercise"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "import skimage\n",
    "import skimage.morphology\n",
    "\n",
    "image_stack = skimage.io.imread('https://cildata.crbs.ucsd.edu/media/images/13585/13585.tif')\n",
    "image_nuclei = image_stack[0:100,0:100,2]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "1. Using the skimage documentation (Google it), try to find the Sobel filter. Try it out on ```image_nuclei``` and by plotting it, try to understand what it does"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "2. Using the Otsu method, make a mask of the filtered image and plot it"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "3. Threy to erode the image. Use influence regions of different sizes and observe the effect:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "4. Choose an erosion level that leaves at least one of the circles complete. Use the skeletonize filter on your resulting eroded mask"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.9.10"
  },
  "toc": {
   "base_numbering": 1,
   "nav_menu": {},
   "number_sections": false,
   "sideBar": true,
   "skip_h1_title": false,
   "title_cell": "Table of Contents",
   "title_sidebar": "Contents",
   "toc_cell": false,
   "toc_position": {},
   "toc_section_display": true,
   "toc_window_display": true
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}