Size of SARS-Cov2 virions in class

© 2021 Tom Röschinger. This work is licensed under a Creative Commons Attribution License CC-BY 4.0. All code contained herein is licensed under an MIT license

This notebook is heavily inspired by this lesson by Justin Bois.

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# Always good to have this
import os

# For numerical computation
import numpy as np
import pandas as pd

# For plotting
import matplotlib.pyplot as plt
import seaborn as sns
import colorcet as cc


# For image analysis
import skimage.io
import skimage.filters
import skimage.morphology
import skimage.segmentation
import skimage.measure
import scipy.ndimage


# This enables high resolution graphics inline
%config InlineBackend.figure_format = 'retina'
sns.set()

First we need to import the image and load it using skimage.

file = "../../data/VeroCells-24hSARS-CoV2_i013.tif"

im = skimage.io.imread(file)

We are going to plot a lot of images in this notebook, so let's write a short function that returns an image given a 2D array.

def plot_image(im, cmap=plt.cm.Greys_r, scale=1):
    "Returns a image representation of a 2D array"
    fig, ax = plt.subplots(figsize=(scale*8, scale*8))
    ax.imshow(im, cmap=cmap, aspect=1)
    ax.grid(False)
    return ax

plot_image(im);