Facilities

Overview

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.

FTIR imaging microscope

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).

Specifications

Maximum sample size:
- Area of standard microscope slide glass, maximum height 20 mm

Spatial resolution:
- 6.25 µm or 25 µm

Spectral resolution:
- 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

FTIR spectrometer

Thermo Scientific™ Nicolet iS5 FTIR spectrometer (https://bit.ly/3aTRIlD) can be used for fast and accurate ATR or transmission measurements.

Accessories:

• iD7 Diamond ATR
• iD1 Transmission accessory

Fig 2: Thermo Scientific™ Nicolet iS5 FTIR spectrometer with iD7 Diamond ATR accessory

Raman imaging microscope

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.

Specifications

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

Lasers:
- 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)

Objective selection:
- 10x
- 50x
- 100x
- 10x water immersion
- 60x water immersion

Spatial resolution:
- 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)

Contact details

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

Prusa 3D Printer

To print prototype 3D parts, the research unit has an original Prusa i3 MK3S 3D printer (https://www.prusa3d.com/original-prusa-i3-mk3/).

Specifications

Workspace (build volume):
- 11.025 cm3 (25 x 21 x 21 cm)

Nozzle:
- 0.4 mm

Minimum layer height:
- 0.05 mm

Supported materials:
- PLA, ABS, and more

Contact details

Location:
Training Required: Basic Training of 3D Printing.

Responsible person:
Dr. Jérôme Thevenot, jerome.thevenot(at)oulu.fi

Material Fees:
Research-related use of the 3D printer is free. Reservation needed. Material cost is personal.

Lab 

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: 

• TEKES (room 262B):  
  • CPU: Intel core i7 7829X @ 3.60GHz 
  • RAM: 64Gb 
  • GPU: Nvidia GeForce GTX 1080 Ti 
    
•   Think Station (room 262B): 
  • CPU: Intel core i7 8700 @ 3.20GHz  
  • RAM: 64Gb 
  • GPU: Nvidia Quadro P4000 
    
• Old Raman (room 2112B): 
  • CPU: Intel Xeon E5-2620 v3 @ 2.40GHz 
  • RAM: 128Gb 
  • GPU: Nvidia NVS 310 
    
• uCT (room 204B): 
  • CPU: Intel Xeon E5-2687W v2 @ 3.40GHz 
  • RAM: 128Gb 
  • GPU: Nvidia Quadro K4000 // Nvidia tesla K20c 

Lab infrastructure 

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. 

Center for Science (CSC) 

The MIPT-unit actively uses CSC cluster resources for research purposes. 

Machine learning infrastructure 

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. 

Network-Attached Storage (NAS)

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.

Click here for full specifications 

Specifications

Digital Densitometry

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

Polarized Light Microscopy

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

Multi-energy X-ray Laboratory

X-Ray Tube (VJX's IXS1203 Mini-Focus):

• VJX's IXS1203 Mini-Focus X-ray tube
• Low power (36W) minifocus tube (focus size = 50 μm) with a 30° opening angle
• The maximum voltage of the tube is 120 kV and the maximum current is 0.3 mA
• The tube is mounted onto an optical perforated plate on which other components of the tomography environment are mounted
• Tube has a polyetherimide (ultem) filtration of less than 2 mm and is fitted with a fixed 3 mm aluminum filter (filtration can be added manually)
• Beam can be collimated to the active area of the X-ray detector

X-Ray detector (XCounter XC-Flite FX15):

• Photon-counting detector
• 0.75 mm thick CdTe layer
• Pixel size of 100 × 100 µm2
• 2 manually adjustable energy thresholds

• A large field-of-view (total active area of 51.3×154.7 mm2, height × width)
• Constructed from 24 tiles, each tile having a 256 × 128-pixel area (height × width) with a 100 µm pixel pitch and a 100 µm gap between tiles

Motorized rotator (Thorlabs , NR360S)

• Mounted on a 90 mm aluminium rail and can be adjusted along the beamline
• The position of the rotator controls the magnification at the detector
• 50kg load capacity
• Resolution: < 1 arcsec
• Speed range: 50°/sec

µCT

Bruker Skyscan 1272 

• Allows three-dimensional ex vivo imaging of mesoscopic samples (maximum diameter = 75mm) 
• Spatial resolution up to ~3µm can be achieved 
• Mechanical testing stage allows conducting tensile tests with real-time X-ray imaging 
• For more details visit the manufacturer's site 

Bruker Skyscan 1176

• Three-dimensional imaging of  small animals and samples with diameter up to ~7cm 
• In vivo imaging for rats, mice, limb imaging for larger animals such as rabbits 
• 4D imaging with respiratory or cardiac synchronization 
• Spatial resolution up to ~9µm can be achieved