Kuopio Biomedical Imaging Unit //
Equipment and analysis

Kuopio BIU equipment consist of three MRI scanners, a SPECT/CT and PET unit, optical, ultrasound and photo acoustic small animal imaging. For MRI most of the contemporary imaging and spectroscopy pulse sequences are available or can be implemented on request. For PET, tracers are available from the local production. 


Kuopio Biomedical Imaging Unit houses three experimental MRI scanners operating at 7 T or 9.4 T.

The 9.4 T/31cm horizontal MRI magnet is suitable for in vivo imaging of small animals up to rabbit size. The system has both Agilent (VNMRj 3.1) and Bruker (PV 5.1 and 6.01) imaging interfaces with all contemporary pulse sequences. The system has 1H and X nuclei (31P, 13C) capabilities for both interfaces. The RF coils for rat and mouse brain and cardiac MRI rely on separate transmitter volume coils combined with up-to 4-channel receiver coils for improved sensitivity.

The magnet is equipped with two gradient sets:

  • 60 G/cm, inner bore diameter 120 mm (small animals: rats, mice, etc.)
  • 30 G/cm, inner bore diameter 210 mm (rabbits, etc.)

The 7 T/16cm horizontal Bruker PharmaScan (PV 5.1 and 6.01) magnet is equipped with all contemporary pulse sequences and is especially suited for external users.

The vertical 9.4 T/89mm magnet is interfaced to Agilent DirectDrive micro-imaging console. The magnet is equipped with 100 G/cm (inner bore diameter 45 mm) actively shielded gradient set for in vivo mouse MRI and microimaging of ex vivo and other samples.

MRI Techniques

All contemporary imaging and spectroscopy pulse sequences are available. In Kuopio we also have more than 20 years’ experience in tailoring MRI experiments for different purposes including pulse-sequence development. Applications of spin-lock contrast methods have been, and still are, one of the specialties of the MR groups lead by Professor Olli Gröhn and Research Director Timo Liimatainen in A.I.Virtanen Institute for Molecular Sciences.

A large variety of different MRI and MRS techniques are available for rodent brain and cardiac imaging, including

  • Anatomical imaging with multiple qualitative and quantitative contrasts (T1, T2, T1rho, T2rho, RAFF, MT)
  • Functional, pharmacological and resting-state MRI with simultaneous electrical measurements
  • Diffusion (tensor) imaging (routinely DW-EPI with 60 directions)
  • Perfusion (CBF/CBV) imaging
  • Ultrashort TE imaging (UTE/ZTE/SWIFT)
  • Short echo time (1-2ms) single voxel spectroscopy (1H, 31P, 13C) and spectroscopic imaging.

Data analysis

Most of our data analysis is done in Matlab. Simple image analysis and calculation of e.g. relaxation time maps is performed using our home-built image analysis interface Aedes. For more complicated computing (Z-spectroscopy, diffusion tensor imaging...), separate Matlab routines are built. Functional and pharmacological MRI data is analyzed in FSL or SPM software and MRS data with LC model.


Kuopio Biomedical Imaging Unit also has positron emission tomography (PET), single photon emission tomography (SPECT) and computed tomography (CT) imaging systems for functional imaging studies. Radiologic imaging with experimental small animals can be used in evaluating metabolic activity, neurotransmitter systems and gene expression and in developing new pharmaceutical products and new targeting molecules (drugs, bioactive peptides and proteins) as well as nanoparticles, viruses and living cells for imaging in e.g. tumors or brain and heart dysfunctions. Animal subjects can be studied over time with repeat measurements on the same animals allowing long term biodistribution studies.

With the Inveon Dedicated PET (Siemens) one rat or up to 4 mice can currently be imaged with PET simultaneously. The detector ring consists of lutetium oxyorthosilicate block detectors, with 10 cm transaxial and 12.7 cm axial field-of-view and reaching ~1.4 mm resolution. It is mainly used for imaging with various 18F- or 11C-labelled biomolecules.

The Flex SPECT/CT (GMI) unit combines functional imaging provided by SPECT, fused with high-resolution anatomical imaging provided by CT. SPECT/CT unit is suitable for imaging of mice, rats and rabbits with 99mTc, 111In, 123I and 125I tracers. The SPECT unit consist of two head detectors with NaI crystals resulting in matrix size 81 x 81 for a 12.5 x 12.5 cm2 field-of-view. The four different collimators include: high resolution and high sensitivity parallel low energy collimators, low energy pinhole collimators with 1.0 mm and 0.5 mm apertures (resolution up to ~1 mm) for 99mTc, 123I and 125I tracers and parallel medium energy collimators for 111In.

The CT unit has a CMOS detector with 50 µm pitch and matrix size is up to 2048 x 2048 for a field-of-view of 10.7 x 10.7 cm2. The maximum voltage of X-Ray tube is 80 kV, and maximum current 1 mA.

Multimodal imaging

We have stereotactic small animal holders that can be used in the 7 T magnet, PET and the SPECT/CT device allowing multimodality (MRI/PET/SPECT/CT) imaging in the same coordinates.

Animal Handling

The Kuopio-BIU facility has complete anesthesia and physiological monitoring units suitable for in-bore monitoring of experimental animals. These units also allow triggering for breathing and heartbeat -synchronized imaging. Lab Animal Centre is easily reachable from the facility and small groups of animals can also be temporarily stored within Kuopio-BIU premises.