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#
Read the jupyter notebooks for this project
Download the materials (see downloads section below)
Run the project yourself (see general instructions)
Background#
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#
Downloads#
Download data, scripts, and template