Focused Ion Beam Scanning Electron Microscopy Image Segmentation

Summary:

  1. SimpleITK supports a large number of filters that facilitate classical segmentation algorithms (variety of thresholding algorithms, watersheds...).
  2. Once your data is segmented SimpleITK enables you to efficiently post process the segmentation (e.g. label distinct objects, analyze object shapes).

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.

In [1]:
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

Load data

Load the 3D volume and display it.

In [2]:
img = sitk.ReadImage(fdata("fib_sem_bacillus_subtilis.mha"))
gui.MultiImageDisplay(image_list = [img], figure_size=(8,4));
Fetching fib_sem_bacillus_subtilis.mha