Quantitative Microscopy

Manual counting of objects and making measurements in microscopy images is very time consuming. Therefore, we develop automatic image analysis methods for microscopy. The images can be two, three, or four dimensional (space + time) and the sources can be light, fluorescence, or electron microscopes. The objects to measure can be biological samples such as viruses and cells, or specific molecular markers, and the purpose diagnostics or quality control. Below are short descriptions of some of our ongoing projects.

== Tissue Analysis and Spatial Omics==
Images result from advanced molecular detection techniques (spatial omics), high content screening, imaging flow cytometry, mass spectrometers and others. We develop image analysis methods and tools to find, count, classify and segment objects of interest and find relationships between structural and molecular information in images. Information is extracted in several levels: genetic, epigenetic, gene expression, protein expression, protein activity and general morphological structure. Studied in different scales: single cells and tissue. Isolated or in-situ. Data analysis results are used directly or to assist pathologists and medical doctors by efficiently displaying large amounts of data in a succinct and smart form.
More information about our visualization tools and analysis methods for spatial omics can be found at TissUUmaps

High Throughput Screening of Zebrafish

The zebrafish Danio rerio is a well-established and effective vertebrate model organism. It is highly complex and possesses discrete organs and tissues and many of the fundamental mechanisms are conserved in humans. Due to its small size, optical transparency of complex organs the zebrafish is well suited for imaging using microscopy and an ideal organism for large-scale screening. We are developing imaging systems for 3D screening of zebrafish using optical projection tomography (OPT) and analysis methods for high-throughput screening of zebrafish using different microscopy imaging modalities.

Automation of Electron Microscopy

Electron microscopy allows for studying the shape and morphology of sub-cellular structures such as proteins and viruses at the nm level. Our current 2D research focuses on developing a miniaturized electron microscope, automated content driven image acquisition, and segmentation and texture measurements for virus diagnostics and nanoparticle analysis. Image to the left: Transmission electron microscopy image of a fecal gastroenteritis patient sample containing Adenovirus.

BioImage Informatics Facility

Connected to the Quantitative Microscopy group is the SciLifeLab BioImage Informatics National Facility. The Facility provides support and education in image analysis to researchers at Swedish Life Science institutes, and has two nodes; one in Stockholm, connected to the School of Computer Science and Communication at KTH, and one in Uppsala, at the Centre for Image Analysis, Dept. of Information Technology, Uppsala University.
https://www.scilifelab.se/facilities/bioimage-informatics/