protists

Open-source virtual microscope lab: real microorganisms, cell cultures and plant tissues whose life emerges from physics (soft bodies, low-Reynolds fluid, chemistry). Reproducible and measurable, for research and teaching.

A collection of datasets and neural networks for microorganism image classification

De nove assembly and annotation of Fragilaria radians transcriptome

Code and plots for the paper of Jauss & Walden et al., 2020, https://www.frontiersin.org/articles/10.3389/fmicb.2020.592189/

Which genomes are where in the big DBs?

Code and plots for the paper of Walden et al., 2021, https://doi.org/10.1093/femsec/fiab081

An e-book about the evolution and diversity of microbial eukaryotes including fungi.

R pipeline for analyzing temperature and CO₂ interactive effects on protist community traits in boreal peatlands using SPRUCE experiment data

Team Goop's 'Iron out the Kinks' Repo

Code to support data analysis for manuscript (doi.org/10.1101/2024.05.12.593719)

Measures testate amoeba tests (shells) from microscope pictures or drawings: finds the scale bar, outline and aperture, then gives length, width, aperture width, neck and ratios, a radial profile and a 250-point outline for geometric morphometrics. Desktop app (Windows, macOS) and command line; every hand correction is recorded.

Contains scripts for biodiversity assessments of European lakes

Salinity as a driver of speciation in free-living dinoflagellates

Code and plots for the paper of Jauss & Nowack et al., 2021: https://doi.org/10.1016/j.ejop.2021.125805

data, code and results from Cerini F., O’Brien DA., Wolfe E., Besson M. and Clements CF. 2023. Phenotypic response to different predator strategies can be mediated by temperature: high-resolution data from protist microcosms.

Protists Survival is an educational arcade-style game where you play as a protist from different eukaryotic supergroups. Your goal is to survive as long as possible by collecting energy and avoiding dangers in a dynamic, scrolling environment inspired by real protist biology.