High-Content Microscopy

National facility


The High-Content Microscopy facility enables researchers to access the resources and expertise from the Human Protein Atlas, by providing high-throughput profiling of protein targets in individual cells using multiplexed immunostaining and fluorescence bioimaging. Based on the resource of more than 37,000 antibodies and a panel of >20 different human cell lines, this facility has a unique position to investigate subcellular spatial proteomics for human and rodent biology. This is ideal for functional validation of discoveries/hits from large-scale omics projects in human cells. For users wanting to image at even higher resolution (STED, SIM etc.), the High Content Microscopy facility can assist in sample preparation and evaluation of suitable antibodies for super-resolution microscopy.

The facility also support study design, image analysis and statistical analysis of data.


  • Automated image analysis.
  • Manual image analysis.
  • siRNA knockdown.
  • Target protein analysis using immunostaining and confocal microscopy. External or HPA antibodies in human or rodent cell lines.

Proposed projects are assessed and prioritized according to the following model.

Initial screen of project by facility:

1. Technical feasibility (yes/no)
2. Capacity requested for the project (classification: small/medium/large)

Project prioritization by committee based on:

1. Scientific potential 0 - 5
2. Supporting preliminary data 0 - 5
3. Supports facility development (competence and techniques) 0 - 5
4. Significance of facility specific technique for project 0 – 2


  • High-throughput profiling of protein targets in single cells using multiplexed immunofluorescence and fluorescent bioimaging.
  • Analysis in cell line of choice or from a standardized panel of >20 human/rodent cell lines.
  • Quantitative image analysis at a single cell level (for example co-localization of targets).
  • siRNA downregulation of target proteins.
  • IF application testing of antibodies.




  • Antibodies. 47,000 antibodies validated (by protein arrays) from the Human Protein Atlas project.
  • Confocal microscope. 3 LEICA SP5 confocal microscopes
  • Liquid handling. Two TECAN FREEDOM EVO 150 pipetting robots. One TECAN Fluent 480.


  • A four-stage isogenic human cell model for malignant transformation was characterized with RNA-seq to identify differentially expressed genes. Subsequent functional analysis of the target proteins in the cell model was done on a single cell level using antibodies and confocal microscopy. We could in this manner characterize the molecular mechanism behind malignant transformation in this model and validate potential novel biomarkers of clinical interest. Danielsson et al, PNAS (Apr 2013).