Microscopy projects
Software, models and hardware for microscopy
The spaCR and Starplast pages are public. The live_cell and Cellect pages are drafts and require a password.
Projects
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spaCR
A Python package and desktop application for image-based pooled CRISPR screens: segmentation, single-cell measurements, annotation, classification, barcode mapping and regression.
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Starplast
A desktop app for exploring gene evidence in Toxoplasma gondii and Plasmodium falciparum: expression, fitness screens, localization, protein features, interactions and literature annotations.
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live_cell
Segmentation models for transmitted-light microscopy.
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Cellect mount
A 3D-printed mount that holds a phone over a microscope eyepiece.
About
This site presents spaCR and related microscopy projects: software, segmentation models and hardware, with the data and code behind each figure.
- Maintainer
- Einar B. Olafsson
- Affiliation
- Research Investigator, Department of Microbiology & Immunology, University of Michigan
- Biography
- Einar B. Olafsson is a Research Investigator in the Department of Microbiology & Immunology at the University of Michigan. He studies how Toxoplasma gondii interacts with the cells it infects, combining CRISPR screening, high-content microscopy and AI-based single-cell image analysis to link genetic perturbations to spatial cellular phenotypes. He created and maintains spaCR. He studied biology and immunology at Uppsala University and received his PhD in Molecular Biosciences from Stockholm University, with a thesis on signalling in Toxoplasma dissemination by infected immune cells.
- Contact
- olafsson@med.umich.edu
- How to cite
- Cite spaCR with its concept DOI 10.5281/zenodo.21343316, which covers all versions, or with the version DOI and BibTeX under Install and cite.