This notebook will illustrate the use of SimpleITK for segmentation of bacteria from a 3D Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) image. The specific bacterium is bacillus subtilis, a rod shaped organism naturally found in soil and plants. The bacteria have been subjected to stress to initiate the process of forming an endospore. These endospores can be seen as a generally dark ellipsoid inside the individual bacterium.
Data provided courtesy of the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health.
import SimpleITK as sitk import pandas as pd %matplotlib notebook import matplotlib.pyplot as plt import gui from math import ceil %run update_path_to_download_script from downloaddata import fetch_data as fdata
img = sitk.ReadImage(fdata("fib_sem_bacillus_subtilis.mha")) gui.MultiImageDisplay(image_list = [img], figure_size=(8,4));