Biologist, Python developer, and creator of spaCR.
I'm Einar B. Olafsson, a Research Investigator in the Department of Microbiology & Immunology at the University of Michigan. I work at the intersection of infection biology, cell biology, and data science, moving between experiments, microscopy, and Python to connect what we see inside cells with the genes behind it.
I'm interested in a simple question with a complicated answer: how do genes shape what happens inside a cell?
My research focuses on host–parasite interactions, particularly those involving Toxoplasma gondii. I study how this parasite changes the behavior of the cells it infects and interacts with their cellular machinery. My work has ranged from immune-cell signaling and migration to the parasite's use of host proteins and pathways.
Today, I combine CRISPR-based screening, high-content microscopy, and AI-based single-cell image analysis to investigate these interactions. The goal is to connect genetic perturbations to spatial cellular phenotypes: where things are inside a cell, how they are organized, and how that organization changes when a gene is disrupted.
I'm also working on bringing image-based CRISPR screens together with spatial transcriptomics, connecting quantitative cellular phenotypes with spatial gene-expression measurements.
I'm the creator and maintainer of spaCR, an open-source Python platform for image-based CRISPR–Cas9 screening and spatial phenotype analysis.
spaCR brings the experimental and computational sides of my work together: using microscopy to capture cellular phenotypes, computational methods to measure them, and genetic screens to investigate their underlying causes. Alongside developing the software, I maintain its documentation, manage releases, and provide user support.
For me, the software is part of the science—a way to turn images into quantitative questions about gene function, and to share the tools used to answer them.
Explore the code · PyPI · Conda-forge
I studied Biology and Immunology at Uppsala University, then completed my PhD in Molecular Biosciences at Stockholm University, investigating the signaling mechanisms involved in Toxoplasma dissemination through infected immune cells.
My postdoctoral training at Stockholm University, the University of Michigan, and Uppsala University brought together parasitology, programming, bioinformatics, and high-content imaging. That combination continues to shape both the biological questions I ask and the software I build.
Teaching and mentoring are also part of my work. I've taught microbiology and infection biology, helped lead practical training in the Biology of Parasitism course at the Marine Biological Laboratory, and mentored students in microscopy and Python-based image analysis. I've also developed teaching materials that connect experimental design, microscopy datasets, and analysis in Jupyter notebooks.
Working on related questions, trying spaCR, or have an idea for a collaboration? I'd be happy to hear from you.