Diversity and evolution of cerebellar folding
Katja Heuer, Nicolas Traut, Alexandra A. de Sousa, Sofie Valk, Roberto Toro.
Data and code accompanying the manuscript "Diversity and evolution of cerebellar folding in mammals".
Neuroanatomical measurements and some complementary external data are provided in CSV files.
Cerebellar and cerebral histological slices used in the analysis are provided as PNG images for convenience.
Vectorial annotations are also provided for convenience as JSON files, and in standard SVG format. The corresponding images are linked with a relative path to the images in the /data/raw/img/ directories. Note: The Finder in MacOS may display the images with a question mark, however, opening them in Inkscape or in a Web browser will show them correctly.
The complete dataset -- images and vectorial annotations -- at the highest resolution available, is accessible through the Web application MicroDraw at https://microdraw.pasteur.fr/project/brainmuseum-cb. The microdraw.py package (https://github.com/neuroanatomy/microdraw.py) provides functions for accessing the MicroDraw dataset, and to extract the phenotypes used in our paper.
All filles in /data/derived/ are generated by code in src. The Python scripts extract the neuroanatomical phenotypes. With an empty /data/derived directory, these scripts should be executed before the R scripts. The R script names indicate the figure/table they produce. The script 7.1_table2_fit_all.R and 7.2_fit_brain.R fit phylogenetic models to the data and take >1h to execute each. Their results are saved to /data/derived, and are required for the execution of the scripts 8_..., etc.
Python code linted using pylint, R code was linted using lintr.