Biological visualization (BioVis)

Regional facility of national interest

BioVis is a Uppsala University facility associated with SciLifeLab focused on microscopy, imaging and flow cytometry: fee-based easy access to state-of the art instruments.

We provide technology and expertise for high-resolution biological imaging, including supporting analytical and preparative technologies. The imaging techniques we offer include brightfield, fluorescence, confocal, multiphoton, superresolution and lightsheet microscopy, as well as electron microscopy and imaging flow cytometry.

For functional and phenotypical single cell analysis we offer two types of flow cytometers. Traditional analytical flow cytometry and imaging flow cytometry. Cell sorting is also available.

Advanced image analysis can be performed on site or in collaboration with the Centre for Image Analysis in Uppsala.


  • Basic service and independent use of BioVis equipment – After a theoretical and practical introduction to each instrument you are free to book and use the equipment available at BioVis. Assistance is available during normal working hours.
  • Consulting. We can help you plan your experiment, execute and analyse you flow and imaging data.
  • Full service. We analyze your microscopy and flow cytometry samples for you.
  • Cell sorting and electron microscopy (TEM) generally only undertaken by BioVis staff. Contact us for more details.
  • Imaging We can set up high throughput single cell image analysis, tile scans for larger specimens, Z-stacks to build 3D images, time-lapse videos.
  • Live imaging for cells, zebra fish and mice.
  • Image analysis – BioVis can offer access to the following softwares Huygens, Imaris, Image J, Zeiss Zen Blue and Zen Black, Cellprofiler, and IDEAS.
  • Flow analysis Access to the following flow cytometry softwares FACSDiva, IDEAS and Modfit.
  • Flow cytometry and cell sorting – Analyse and sort cells into tubes or plates for downstream analysis. Down to single cells into 96 or 384 well plates and bulk sort into up to four tubes. Temperature control available, +4°C to +42°C. Cell incubator available.
  • Sample preparation. Embedding and sectioning of biological samples for electron microscopy (TEM). Service also includes imaging and analysis.
  • Courses – BioVis regularly offers courses: Confocal Microscopy, Flow Cytometry and Image Analysis. See our webpage for a full list of courses.
  • Visits & Outreach we can organize a short presentation of relevant techniques at your department. Contact us for more information.
  • Image analysis available in collaboration with the Centre for Image Analysis (CBA) in Uppsala.


  • Co-localization studies on both cell- and tissue levels with several simultaneous markers
  • Ultrastructural morphology and IHC studies
  • Analysis of the 3D-distribution of markers of interest in the cell or cell environs
  • Intravital microscopy
  • Quantitative analysis of cell populations and marker expression
  • Preparative experiments to isolate cells or tissue sections of interest for downstream processing


  • Merck Amnis FlowSight Imaging Flow cytometry (nm 405, 488, 562, 633, 785)
  • BD FACS Aria III Flow Cytometry and cell sorting (nm 405, 488, 562, 633)
  • BD LSR Fortessa Flow Cytometry (nm 355, 405, 488, 562, 640) FSC-PMT detector for small particles.
  • Zeiss LSM700 confocal microscope (nm 405, 488, 555, 633)
  • Zeiss 710/ NLO confocal / multiphoton microscope. (nm 488/514, 543, 633, MaiTai 690-1040)
  • Zeiss 710/SIM confocal / superresolution microscope (nm 405, 488/514, 561, 633).
  • Zeiss AxioImager M2 brightfield and fluorescence microscope.
  • Zeiss Lightsheet Z.1. (nm 405, 488, 561, 633) including chamber for optically cleared tissue (R.I. 1.45)
  • Zeiss Stereomicroscope
  • FEI Tecnai G2, Transmission Electron Microscope (TEM)