A long-standing focus of the research unit is to develop new methods and protocols for visualizing the biological tissues and evaluating their biochemical properties to solve deeply rooted problems in musculoskeletal disease and cancer research.
For these purposes, our research unit has a Fourier transform infrared (FTIR) and a Raman imaging microscope located on the second floor of Kieppi (Aapistie 5A) in the room 2128B.
Thermo Scientific Nicolet iN10 FTIR imaging microscope (https://bit.ly/2ydr9Ld) can provide spectral information about the chemical composition within samples. The device is equipped with a motorized stage, which provides ease of use in finding desired areas of the sample and allows the mapping of large areas. Measurement mode can be selected between transmission (transparent samples, e.g. thin tissue slices) and reflection (smooth surfaces, thin coatings, solids, and powders).
Maximum sample size:
- Area of standard microscope slide glass, maximum height 20 mm
- 6.25 µm or 25 µm
- 2 cm-1
Spectral resolution and range:
- Room temperature DTGS detector, spectral range 7600 – 450 cm-1
- Liquid nitrogen cooled high sensitivity MCT-A detectors
- Single element spectral range 7800 – 650 cm-1
- Multiple (16) element spectral range 7800 – 715 cm-1
Fig 1: Thermo Scientific Nicolet iN10 FTIR imaging microscope
Thermo Scientific™ Nicolet iS5 FTIR spectrometer (https://bit.ly/3aTRIlD) can be used for fast and accurate ATR or transmission measurements.
Fig 2: Thermo Scientific™ Nicolet iS5 FTIR spectrometer with iD7 Diamond ATR accessory
The research unit has a Thermo Scientific DXR2xi Raman imaging microscope (https://bit.ly/2xt7c2n). Coupled with the Thermo Scientific™ OMNIC™xi Software, the instrument can be used for spectroscopic characterization of a wide variety of materials including biological tissue with minimal or no sample preparation.
Maximum sample size:
- With high-precision motorized stage (step size 0.1 µm): 100 mm × 75 mm travel X and Y dimensions; height ~40 mm
- 532 nm (max power: 10 mW)
- 785 nm (max power: 30 mW)
Spectral resolution and range:
- Full-range grating (resolution: 5 cm-1, range: 50 – 3500 cm-1)
- High-resolution grating (resolution: 2 cm-1, range: 50 – 1800 cm-1)
- 10x water immersion
- 60x water immersion
- Resolution (X, Y axes) with high-precision motorized stage: < 1 µm (laser spot size depends on the laser and objective)
- Confocal depth resolution (Z axis): < 2 µm
Figure 1: Thermo Scientific DXR2xi Raman imaging microscope
Figure 2: Raman microspectroscopic analysis of the tissue-specific composition of the human bone-cartilage junction (https://doi.org/10.1016/j.actbio.2020.02.020)
To request training or data collection using the FTIR and/or Raman system, please contact
Dr. Lassi Rieppo (lassi.rieppo(at)oulu.fi).
Staffs or students of the University of Oulu can also reserve the spectroscopic systems by using this link: http://www.asimov.fi/oulu/reservation/index.php
To print prototype 3D parts, the research unit has an original Prusa i3 MK3S 3D printer (https://www.prusa3d.com/original-prusa-i3-mk3/).
Workspace (build volume):
- 11.025 cm3 (25 x 21 x 21 cm)
- 0.4 mm
Minimum layer height:
- 0.05 mm
- PLA, ABS, and more
Training Required: Basic Training of 3D Printing.
Dr. Jérôme Thevenot, jerome.thevenot(at)oulu.fi
Research-related use of the 3D printer is free. Reservation needed. Material cost is personal.
Kieppi 3rd floor:
“ASTRA” has a Quadro P6000 24GB GPU (granted to us by NVIDIA), 16GB RAM, and an Intel Xeon e51620 v3 CPU
“AIDMEI” has two RTX 2080Ti 11GB GPUs, 64GB RAM, and an AMD Ryzen Threadripper 2950X CPU
Kieppi 2nd floor:
The laboratory computational resources consist of a total of 6 personal computers from high- to top-tier performance. Equipment ranges from multi-core CPUs, 16-128GB of RAM and GPUs of varying performance. The computers have approximately 1TB of storage space and access to various network drives for extended space.
The MIPT-unit actively uses CSC cluster resources for research purposes.
The computational resources comprise 10 personal computers (high- to top-tier), each equipped with a powerful multi-core CPU, 1-2 high performance GPUs, 32-64GB of RAM, and 1TB or more of local storage space. These computers can be used to develop solutions for a wide range of medical imaging problems and also to prototype the most computationally-heavy algorithms for their further training and implementation on the CSC cluster.
To support local analysis of large-scale medical datasets, we employ a NAS system with 46.8 TB of fully backed up storage space. The NAS is run by Dell PowerEdge R320 rack server with uninterruptible power supply system.
Three high-performance computers are intended for student use and can be reserved. For details, contact Santeri Rytky, santeri.rytky(at)oulu.fi
For mechanical testing, we have Instron 3366 mechanical tester with two different load cells and multiple sample holders for different types of measurements.
|Measurement accuracy (1/200 step)||±0.25N||±0.0125N|
|Measurement accuracy (1/200-1/500 step)||±0.5N||±0.025N|
|Testing speed range||0.005-500mm/min||0.005-500mm/min|
|Horizontal test space||420mm||420mm|
|Vertical test space||1193mm||1193mm|
MIPT facilities include Carl Zeiss Axio Scope A1 microscope with a QImaging QICAM camera used for digital densitometry (DD) analysis. The system utilizes bandpass filters to quantitatively measure certain wavelength monochromatic light present in histological staining protocols. Our DD system is equipped with 3 different bandpass filters are utilized for quantitative analysis of different staining protocols:
- Masson’s trichrome: 625 nm
- Picrosirius red: 550 nm
- Safranin-O: 492 nm
Our facilities have Nikon Diaphot TMD microscope equipped with Abrio PLM imaging system. The Abrio system consists of a green bandpass filter, a circular polarizer, and a computer-controlled analyzer composed of two liquid crystal polarizers, and a CCD camera. The system can be used for automated measurement of the magnitude of retardance in birefringent materials such as tissue sections.
Figure 1. Safranin O, cluster and PLM images from three samples with different severity of OA. The corresponding cluster images from the carbohydrate region are extracted from the combined hyperspectral data.
Figure adapted from: Oinas, J., Rieppo, L., Finnilä, M. et al. Imaging of Osteoarthritic Human Articular Cartilage using Fourier Transform Infrared Microspectroscopy Combined with Multivariate and Univariate Analysis. Sci Rep 6, 30008 (2016). https://doi.org/10.1038/srep30008
Figure 2. Correlations between the DD or PLM and FTIR-derived collagen contents at different layers of cartilage.
Figure adapted from: Rieppo L, Janssen L, Rahunen K, Lehenkari P, Finnilä MAJ, Saarakkala S. Histochemical quantification of collagen content in articular cartilage. PLoS One. 2019;14(11):e0224839. Published 2019 Nov 7. doi:10.1371/journal.pone.022483
X-Ray Tube (VJX's IXS1203 Mini-Focus):
X-Ray detector (XCounter XC-Flite FX15):
Motorized rotator (Thorlabs , NR360S)