Specialized Microscopy Systems at BIC

The BIC facility has several specialized microscopy systems that are optimized for various applications.

Evident Alpha3 Light Sheet Microscope, Facility Edition

The light-sheet microscope from Evident (former Olympus) is for whole-tissue imaging using cleared transparent tissue.


  • Laser lines (nm): 405, 488, 561, 638, 730.
  • Objectives: 2X, 4X, 10X, 25X (3.250, 1.625, 0.650, and 0.260 micrometer/pixel resolution). WD = 8 mm for all objective lenses.
  • Illumination, 2X, 5X, 10X (9, 4, and 1.5 micrometer optical thickness each)
  • Extra: Tiling, Real-time focus sweeping, Dynamic focus for multi-color imaging, Shading correction. Chamber volume 240 ml
  • Software: QtSPIM
LaVision Light-Sheet Microscope is included in BIC's equipment and is for whole tissue imaging and optimised for organic solvent-based clearing methods.
LaVision Light-Sheet Microscope. Photo: Anna Kouznetsova

LaVision Light-Sheet Microscope

The light-sheet microscope from LaVision Biotec (UltraMicroscope II) is for whole tissue imaging using cleared transparent tissue. The microscope is optimized for organic solvent-based clearing methods such as 3DISCO (iDisco).


  • Laser lines (nm): 405, 488, 561, 639, 785
  • Objectives: 2X with 0.63X to 6.3X adjustment (total magnification is 1.26X to 12.6X), WD = approximately 5.6 mm
  • Extra: Tiling and Dynamic horizontal focus. For long working distance objectives (1.1X, 4X, 12X), please contact the BIC facility
  • Software: ImSpector and TeraStitcher for stitching
The LSM 510-NLO is a laser point-scanning confocal system based on Zeiss Axioplan 2 imaging model upright microscope with a motorised x/y stage.
Zeiss LSM510 NLO Microscope (2-photon). Photo: Anna Kouznetsova

Zeiss LSM510 NLO Microscope (2-photon)

The LSM 510-NLO is a laser point-scanning confocal system based on the Zeiss Axioplan 2 imaging model upright microscope with a motorised x/y-stage.


  • Laser lines (nm): 670-1080, 488, 515, 561, 594, 647
  • Objectives: 20x Objective, NA=1.0, working distance 8 mm, 40x Objective, NA=0.8, working distance 6 mm
  • Extra: Coherent Cameleon UltraII, E-phys
  • Software: Zen black
A spatial transcriptomics platform based on a Vizgen Merscope platform.
MERSCOPE. Photo: Anna Kouznetsova

Vizgen MERSCOPE Spatial transcriptomics

MERSCOPE from Vizgen is a specialized imaging system designed for spatial transcriptomics imaging, driven by MERFISH (Multiplexed Error-Robust Fluorescence in situ Hybridization) technology. MERFISH technology is built upon an RNA imaging-based technique called single molecule FISH and combinatorial barcoding scheme. This technique identifies nucleic acids in their native tissue environment with sub-cellular resolution.  

To utilize MERSCOPE, you need to order a gene panel from Vizgen, choosing from pre-designed or custom panels for 140, 300, 500 or 1000 genes, depending on your research needs. The current MERSCOPE  offer predesigned gene panels for both mouse and human species. For other species, custom design panel is required. Compatible tissue is fresh or fixed frozen sections, cell cultures, and FFPE samples prepared on specialized Vizgen slides. 

The instrument training and booking can be done by mail bic@ki.se. We offer training using the MERSCOPE Sample Verification Kit for mouse or human tissue. The training can be done with your samples or our practice sample. Please note that the sample must be mounted on Vizgen slides, the sections mounted on common slide glass are not compatible. 

We strongly recommend reaching out to us before placing an order for a gene panel to ensure the instrument’s availability at the time you prefer. Each instrument run is time-consuming, and we cannot guarantee time slots on the instrument unless we are informed about your planned experiment in advance.

For all questions, please contact bic@ki.se.

Choosing a microscope and where to find it

If you are interested in more details, we have compiled detailed information about our instruments. The information could be useful when choosing between different microscopes.

You are always welcome to contact us if you need further information or guidance among the microscopes.

Where to find our instruments.