Counting isopods#

In this project the goal is to measure measure phenotypic distributions of several specimens of isopods (Asellus aquaticus) using the threshold algorithm. We also use image registration to find a reference card and automatically size and color-correct the image.


Get started#

  1. Read the jupyter notebooks for this project

  2. Download the materials (see downloads section below)

  3. Run the project yourself (see general instructions)


This workflow was used for a master’s project where we quickly needed to measure the phenotypic distribution (pigmentation as gray scale, and size) before adding multiple batches of live isopods to a predation experiment. Since the isopods were alive and were needed for the experiment, we didn’t use a macro-lens but the default wide angle lens.


Details about the imaging gear and protocol can be found a blog entry on my personal website. We photographed the isopods on a camera stand using a computer controlled Canon EOS 750d DLSR with a 15-45mm lens and LED light panels for better illumination. Imaging each batch took about 20-30 seconds, and processing in phenopype roughly 30 seconds per image.

Jupyter notebooks#

Jupyter notebook

Read a static html render of a jupyter notebook


Project materials

Download data, scripts, and template