Counting snails#

In this project thresholding and watershed algorithms are applied to count freshwater snails, and quantify shape and shell-pigmentation of individual snails.


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)


In this project, first, a mask is set around tray, the reference is set manually (the detection algorithm only works on reference cards with clear boundaries, and not on “continuous” mm-paper), and then thresholding and watershed algorithm are applied. Remaining overlap is removed with the edit_contour tool, and detect_contour is used a once more to determine the final specimen contours. In the second step, the configuration file is modified to add compute_shape_featues and compute_texture_features, followed by a “silent run” feedback=False.

Jupyter notebooks#

Jupyter notebook

Read a static html render of a jupyter notebook


Project materials

Download data, scripts, and template