BioMediTech Research Infrastructure

Tampere Imaging Facility (TIF)

The facility offers state-of-the-art equipment for mesoscopic and high resolution imaging of tissues, small model organisms, biomaterials, tissue engineering products and advanced cell cultures both in 2D and 3D thus offering services for both life scientists and biomedical engineers.

Introduction

Tampere Imaging Facility (TIF) is located in the Arvo building on the Kauppi campus of the University of Tampere. It offers state-of-the-art imaging solutions for life and material scientists. TIF includes several microscope systems for imaging of living or fixed specimens: spinning disk and laser scanning confocal microscopes, super-resolution structured illumination microscope, long timelapse imaging systems and widefield fluorescence microscopes. TIF also has data processing and analysis stations available with deconvolution, visualization and image quantification possibilities.

TIF provides training for users, organizes imaging related courses and actively participates teaching at the University of Tampere and the Tampere University of Technology. Users have the possibility to plan and conduct the experiments and data analysis together with the core personnel.

ACKNOWLEDGEMENT

All the users of Tampere Imaging Facility (TIF) services are obligated to acknowledge the facility in publications:

“The authors acknowledge Tampere Imaging Facility (TIF) for their service.”

Microscopy Systems

Superresolution Microscopes

Nikon N-SIM Super-Resolution System

Nikon N-SIM super-resolution system

User-friendly Nikon N-SIM super-resolution system for visualizing cellular structures and molecular activity with the twice resolution of conventional optical microscopes. Photo: Jonne Renvall/University of Tampere

N-SIM (Nikon Structured Illumination Microscopy) super-resolution system for fixed and living samples. N-SIM doubles the resolution of conventional optical microscopes; resolution will depend on laser wavelength and imaging mode. This system is combined with Nikon A1R+ Laser Scanning Confocal Microscope.

Features:

Nikon Eclipse Ti2-E inverted microscope
Motorized XY stage with encoders
MCL Piezo Stage Insert and Z drive
Large incubator with heating
Stage-top incubator with heating and CO2
Perfect Focus System®

Super-Resolution:

Lateral (XY): ~100-130 nm (dependent on wavelength and optics)
Axial (Z): ~300 nm (dependent on wavelength and optics)
3D Axial Range: up to 20 μm (~8 µm oil, ~20 µm water)
Resolution depends on dye properties

Objectives:

Nikon Plan Apo VC 20x DIC N2, N.A. 0.75, WD 1.00 mm (Air)
Nikon Plan Apo λ 60x Air, N.A. 0.90, WD 0.20 mm (Air)
Nikon CFI Plan Apo IR SR 60x WI, N.A. 1.27, WD 0.17 mm (Water)
Nikon Apo 60x Oil λS DIC N2, N.A. 1.40, WD 0.14 mm (Oil)
Nikon CFI Apo SR TIRF 100X Oil, N.A. 1.49, WD 0.12 mm (Oil)
Nikon SR HP Plan Apo 100x Sil, N.A. 1.35, WD 0.30 mm (Silicone)

Lasers:

Solid state 405 nm, 488 nm, 561 nm, 640 nm lasers built-in AOTF (Acousto-Optical Tunable Filter)

Transmitted Light:

DIC

N-SIM Camera and filters:

EM CCD camera iXon3 DU-897E (Andor Technology Ltd.)
N-SIM CH Filter Cubes for 405, 488, 561, 640

Software:

NIS-Elements C with module software NIS-A N-SIM Analysis

Confocal Microscopes

Nikon A1R+ Laser Scanning Confocal Microscope

NIS-Elements C

NIS-Elements C’s dedicated interface for confocal imaging systems supplied with efficient volume viewer tool for 3D visualization. Photo: Jonne Renvall/University of Tampere

Laser scanning confocal imaging system for fixed and living samples. Incubation and hardware based autofocus (Perfect Focus System®). In addition to galvano scanner, equipped with a resonant scanner for capturing confocal images at high-speed.

Features: 

Nikon Eclipse Ti2-E inverted microscope
Motorized XY stage with encoders
MCL Piezo Stage Insert and Z drive
Large incubator with heating
Stage-top incubator with heating and CO2
Perfect Focus System®
A1R+ equipped with both fast resonant and high-resolution galvano scanners
FRAP/FLIP/Photoactivation possibility
Holders for sliders, dishes, and multiwell plates 

Objectives:

Nikon Plan Apo VC 20x DIC N2, N.A. 0.75, WD 1.00 mm (Air)
Nikon Plan Apo λ 60x Air, N.A. 0.90, WD 0.20 mm (Air)
Nikon CFI Plan Apo IR SR 60x WI, N.A. 1.27, WD 0.17 mm (Water)
Nikon Apo 60x Oil λS DIC N2, N.A. 1.40, WD 0.14 mm (Oil)
Nikon CFI Apo SR TIRF 100X Oil, N.A. 1.49, WD 0.12 mm (Oil)
Nikon SR HP Plan Apo 100x Sil, N.A. 1.35, WD 0.30 mm (Silicone) 

Lasers:

Solid state 405 nm, 488 nm, 561 nm, 640 nm lasers built-in AOTF (Acousto-Optical Tunable Filter)

Detectors and Filters:

A1-DUG GaAsP Multi Detector Unit: 2 GaAsP PMTs + 2 normal PMTs
Emission filters: 450/50, 482/35, 525/50, 540/30, 595/50, 700/75

Transmitted Light: 

DIC

Software:

NIS-Elements C with module software NIS-A N-SIM Analysis

Nikon Spinning Disk Confocal Microscope

Nikon Spinning Disk

Nikon Spinning Disk laser scanning confocal microscope is tool for rapid spatial and temporal imaging of living cells. Photo: Jonne Renvall/University of Tampere

Laser scanning confocal imaging system for fixed and living samples. Equipped with incubation chamber and hardware based autofocus (Perfect Focus System®).

Features:

Nikon Eclipse-Ti-E inverted microscope
Large incubator with heating
Stage-top incubator with heating and CO2
Motorized stage from Prior allowing multipoint imaging
Holders for sliders and dishes

Objectives:

Nikon Plan Fluor 10x/0.30, WD 16.0 mm (Air)
Nikon Plan Apo 10x/0.45, WD 4.0 mm (Air)
Nikon Plan Fluor 20x/0.50, WD 2.0 (Air)
Nikon Apo LWD 40x/1.15, WD 0.61 mm (Water)
Nikon Plan Apo 60x/1.40, WD 0.13 mm (Oil)
Nikon Plan Apo 100x/1.40, WD 0.13 mm (Oil)

Lasers and Filters:

Diode-pumped solid-state lasers (DPSSLs): 405 nm, 488 nm, 561 nm and 640 nm

6 different emission filters for the commonly used fluorophores and fluorescent proteins:
Semrock 440/521/607/700 nm BrightLine® quad-band bandpass filter
Semrock 447/60 nm BrightLine® single-band bandpass filter
Chroma ET500lp single-band longpass filter
Chroma Technology ET525/50m single-band bandpass filter
Chroma Technology 607/45m-2P single-band bandpass filter
Chroma Technology ET700/75m single-band bandpass filter

Transmitted Light:

DIC

Camera:

Andor’s Neo 5.5 sCMOS vacuum cooled camera

Software:

Andor iQ 3.0

Zeiss LSM 700 Laser Scanning Confocal Microscope

Zeiss LSM 700

Zeiss LSM 700 provides a simple configuration for laser scanning confocal microscope using spectral imaging. Photo: Jonne Renvall/University of Tampere

LSCM for spectral imaging of fixed samples. User friendly design, simultaneous detection of three color signals. Separation of the fluorescence signals by selective laser excitation coupled to efficient splitting of the emission using the variable secondary dichroic (VSD) beamsplitter.

Features:

Zeiss Axio Observer.Z1 inverted microscope
Motorized Z-drive operation
Mounting frame for specimen sliders 76×26 mm

Objectives:

Zeiss EC Plan-Neofluar 5x/0.16, WD 18.5 mm (Air)
Zeiss EC Plan-Neofluar 10x/0.30, WD 5.2 mm (Air)
Zeiss EC Plan-Neofluar 20x/0.50, WD 2.0 mm (Air)
Zeiss EC Plan-Neofluar 40x/0.75, WD 0.71 mm (Air)
Zeiss Plan-Apochromat 63x/1.40, WD 0.19 mm (Oil)

Lasers and filters:

Solid state diode lasers: 405 nm, 488 nm, and 555 nm

Zeiss Filter set 01: BP 365/12, FT 395, LP 397
Zeiss Filter set 09: BP 450-490, FT 510, LP 515
Zeiss Filter set 15: BP 546/12, FT 580, LP 590

Detector:

2 channel spectral detection with high-sensitivity PMT detector

Software:

ZEN 2009

Zeiss LSM 780 Laser Scanning Confocal Microscope

Zeiss LSM 780

Zeiss LSM 780 is flexible and sensitive spectral confocal laser scanning microscope for various applications. Photo: Jonne Renvall/University of Tampere

LSCM for fixed and living samples. Equipped with spectral detector (no conventional filters) using sensitive GaAsP-technology. In addition to standard lasers the system has tunable InTune-laser, which allows free selection of excitation wavelengths. Fluorescence Correlation Spectroscopy (FCS), FRAP/FLIP/Photoactivation possibility.

Features:

Zeiss Cell Observer.Z1 inverted microscope
Large incubator with heating
Stage-top incubator with heating and CO2
Motorized stage for multipoint imaging
Fluorescence Correlation Spectroscopy (FCS) possibility
Tunable pulsed laser
Holders for sliders, dishes, and multiwell plates

Objectives:

Zeiss Plan Apo 10x/0.45, WD 2 mm (Air)
Zeiss LD LCI Plan-Apochromat 25x/0.80, WD 0.57 mm (Water, Glycerine, Oil)
Zeiss C Apo 40x/1.1, WD 0.62 mm (Water)
Zeiss Plan Apo 40x/1.4, WD 0.24 mm (Oil)
Zeiss Plan Apo 63x/1.4, WD 0.19 mm (Oil)
Zeiss C Apo 63x/1.2, WD 0.28 mm (Water)

Lasers and filters:

Multiline Argon laser: 458 nm, 488 nm, and 514 nm
Diode lasers 405 nm, and 561 nm
HeNe-lasers 594 nm, and 633 nm
InTune-tunable pulsed laser: 490 nm – 645 nm

Detector:

32-channel QUASAR GaAsP PMT array: quantum Efficiency 45 %, excitation range 355 – 660 nm

Software:

ZEN 2012

Structured Illumination Microscopes

Zeiss Apotome.2 Upright Fluorescence Microscope

Zeiss ApoTome.2

Zeiss ApoTome.2 stands for high axial resolution with good signal-to-noise ratio and increases the resolution in Z direction compared to conventional widefield. Photo: Jonne Renvall/University of Tampere

Fluorescent microscope with structured illumination for fixed samples. Ability to create optical sections of your fluorescent samples – free of scattered light. Apotome.2 recognizes the magnification and moves the appropriate grid into the beam path. The system then calculates your optical section from three images with different grid positions to prevent scattered out-of-focus light.

Features:

Axio Imager.M2 upright microscope
Motorized stand with Z-drive
Specimen holder for slides 76×26 mm
LED illumination for epi-fluorescence and transmitted-light

Objectives:

Zeiss EC Plan-Neofluar 2.5x/0.075, WD 9.5 mm (Air)
Zeiss EC Plan-Neofluar 5x/0.16, WD 18.5 mm (Air)
Zeiss EC Plan-Neofluar Ph 1 10x/0.30, WD 5.2 mm (Air)
Zeiss EC Plan-Neofluar Ph 2 20x/0.50, WD 2.0 mm (Air)
Zeiss EC Plan-Neofluar Ph 3 40x/ 1.30, WD 0.21 mm (Oil)
Zeiss Plan-Apochromat 63x/1.40, WD 0.19 mm (Oil)

Light sources and filters:

Light-emitting diodes (LEDs) for Colibri: 380 nm, 470 nm, 555 nm and 625 nm

Zeiss Filter Set 05: EX BP 395-440, BS FT 460, EM LP 470
Zeiss Filter Set 38 HE: EX BP 470/40, BS FT 495, EM BP 525/50
Zeiss Filter Set 56 HE: EX BP 470/27, BP 556/25; BS DFT 490 + 575; EM DBP 512/30 + 630/98
Zeiss Filter Set 62 HE: EX BP 370/40, BP 474/28, BP 585/35; BS TFT 395 + 495 + 610; EM TBP 425 + 527 + LP615
Zeiss Filter set 63: EX BP 572/25, BS FT 590, EM BP 629/62

Transmitted Light:

Brightfield
Phase Contrast
DIC

Camera:

Zeiss AxioCam HRm monochrome camera

Software:

ZEN 2012

Timelapse Imaging Systems

CM Technologies Cell-IQ® Automated Imaging and Analysis System

CM Technologies Cell-IQ®

CM Technologies Cell-IQ® is a fully integrated, automated imaging and analysis system for short and long term timelapse studies of living samples. Photo: Outi Paloheimo/University of Tampere

Cell-IQ® is automated cell culture and analysis system for kinetic cell studies. Operating Cell-IQ is simple requiring minimum set up. LED illumination for both phase and fluorescence imaging reducing external cell effects such as photo-toxicity and photobleaching.

Features:

The system comprises incubator with heating
Independent gas feeds up to two multiwell plate positions
Compatible with 6-, 12-, 24-, 48-, and 96-well microplates
Autofocus and Z-stack possibility

Objectives:

Nikon Plan Fluor 4x/0.13, WD 16.5 mm (Air)
Nikon Plan Fluor 10x/0.30, WD 15.2 mm (Air)
Nikon S Plan Fluor ELWD 20x/0.45, WD 8.2−6.9 mm (Air)
Nikon S Plan Fluor ELWD 40x/0.60, WD 3.6–2.8 mm (Air)

Light sources and filters:

PE Excitation system with LED light source (470 nm, 550 nm, 660 nm)

Semrock Filter set GFP/488 (LF488): EX BP 482/9, EM LP 505, DM RB 471−491 (longpass)
Semrock Filter set Cy3-C/568 (LF561/LP-A-000): EX BP 561/7, EM LP 585, DM RB 554−568 (longpass)
Semrock Filter set Cy5-C/680 (Cy5.5-B-000): EX BP 655/20, EM BP 716/20, DM RB 350−676 (bandpass)

Transmitted Light:

Phase Contrast

Camera:

Retiga EXi 1392 CCD monochrome camera

Software:

Cell-IQ ImagenTM

Image Processing Software:

Cell-IQ AnalyserTM

Nikon BioStation CT Automated Imaging and Analysis System

Nikon BioStation CT

Nikon BioStation CT moves multiwell plates between the microscope stage and the vessel rack via a robotic device. Photo: Outi Paloheimo/University of Tampere

Cell observation incubator with an inverted microscope inside, maintaining precise levels of CO2, humidity, and temperature. BioStation CT provides apodized phase contrast (APC) optics and three color LED illumination for fluorescence with magnifications from 2x to 40x.

Features:

Incubator with controlled humidity and CO2 environment
Robotic arm transfers cell plates to microscope from holder racks
Autofocus and Z-stack possibility
Stage travel XY: 120 x 90 mm, Z: 4 mm
For 75cm2 flasks and multiwell plates: 6-, 12-, 24-, 48- and 96-well plates
Capacity up to 30 well plates simultaneously

Objectives and magnification:

Magnifications: 2x, 4x, 10x, 20x, 40x
Objectives: Nikon Plan Apo DLL 4x/0.20 (Air), Nikon Plan Fluor ADL 10x/0.30 (Air)

Light sources and filters:

Phase contrast: high-intensity red LED illumination, automatic phase ring changeover
Epi-fluorescence: LED V/B/W illumination

Semrock GFP-3035D-000: BrightLine® single-band filter set, optimized for Green Fluorescent Protein
Semrock TxRed-4040C-000: BrightLine® single-band filter set, optimized for Texas Red
Semrock Cy5-4040C-000: BrightLine® single-band filter set, optimized for Cy5

Transmitted Light:

Phase Contrast

Camera:

2/3-inch cooled CCD camera

Software:

No special application software; PC operation (BioCT-PC Ver. 4.0) with touch panel LCD

Image Processing Software:

Nikon CL-Quant

Widefield Fluorescence Microscopes

Nikon AZ100 Upright Fluorescence Macroscope

Nikon AZ100 fluorescence macroscope

Nikon AZ100 fluorescence macroscope objective lineup consists of 1x, 2x, and 5x lenses covering visualization from low to medium magnifications. Photo: Jonne Renvall/University of Tampere

The AZ100 is a multi-purpose zoom microscope system for fixed and living samples. Smooth zooming mechanism and a triple nosepiece enables continuous switching of magnifications, extending from macro to micro observation of the same specimen.

Features:

Nikon AZ100 Multizoom upright microscope
Built-in 8x zoom optics, which provide from 1x to 8x magnification
Stand section offers an 85 mm and the stage section a 10 mm stroke; even tall samples can be observed

Objectives:

Nikon AZ-Plan Apo 1x/0.10, WD 35.0 mm (Air)
Nikon AZ-Plan Fluor 2x/0.20, WD 45.0 mm (Air)
Nikon AZ-Plan Fluor 5x/0.50, WD 15.0 mm (Air)

Light sources and filters:

C-FI Plastic Fiber Optics Bifurcated 100 W halogen illuminator
C-HGFI Precentered Fiber epifluorescence 100 W mercury illuminator

Semrock FF01-520/35-25: 520/35 nm BrightLine® single-band bandpass filter
Semrock FF01-543/22-25: 543/22 nm BrightLine® single-band bandpass filter

Transmitted Light:

Brightfield

Camera:

The Imaging Source DFK 33UX250 CMOS color camera

Software:

NIS-Elements D

Olympus BX61WI Fluorescence Water Immersion Microscope (Note: Currently not in use!)

Olympus BX61WI water immersion objectives

Olympus BX61WI water immersion objectives provide long working distance with excellent DIC and fluorescence. Photo: Outi Paloheimo/University of Tampere

Widefield fluorescence microscope for fixed and living samples in buffer, media or water. Olympus water immersion microscopes reduces user-induced vibrations. All operational controls are located far from the specimen further prevent concussions. Special swing and swing/slide nosepieces facilitate gentle movement of objectives.

Features:

Olympus BX61WI upright microscope
Fixed-stage and motorized
Integrated motorized high-precision Z-drive

Objectives:

Olympus UMPLFLN10XW 10x/0.30, WD 3.5 mm (Water)
Olympus UMPLFLN20XW 20x/0.50, WD 3.5 mm (Water)
Olympus LUMPLFLN40XW 40x/0.80, WD 3.3 mm (Water)
Olympus LUMPlanFL100XW 100x/1.00, WD 1.5 mm (Water)

Light sources and filters:

High pressure 100 W mercury burner and 100 W halogen illumination

Olympus U-MNUA2: EX BP 360-370, EM BP 420-460, DM 400 (bandpass)
Olympus U-MWIBA3:  EX BP 460-495, EM BP 510-550, DM 505 (bandpass)
Olympus U-MNG2: EX BP 530-550, EM 590, DM 570 (longpass)

Transmitted Light:

Brightfield
DIC

Camera:

Hamamatsu Digital Camera ORCA-ER

Software:

Olympus CellM & CellR Software Version 2.0

Olympus IX51 Inverted Fluorescence Microscope

Olympus IX51 fluorescence microscope

Olympus IX51 fluorescence microscope is user-friendly system with long working distance optics, frame stability, ergonomic layout and low-positioned controls. Photo: Outi Paloheimo/University of Tampere

Widefield fluorescent microscope for fixed samples. User-friendly system specially when long working distance is needed; operating with multiwell plastic plates as well as with glass objective slides.

Features:

Olympus IX51 inverted microscope
Stage holder for multiwell plates
Specimen holder for slides 76×26 mm

Objectives:

Olympus UPlanFL N 4x/0.13, WD 17.0 mm (Air)
Olympus CPlanFL N 10x/0.30, WD 9.5 mm (Air)
Olympus LUCPlan FL N 20x/0.45, WD 6.6−7.8 mm (Air)
Olympus LUCPlan FL N 40x/0.60, WD 3.0−4.2 mm (Air)

Light sources and filters:

High pressure 100 W mercury burner and 30 W halogen illumination

Olympus U-MNU2: EX 360-370, EM 420, DM 400 (longpass)
Olympus U-MNUA2: EX 360-370, EM 420-460, DM 400 (bandpass)
Olympus U-MNIBA3: EX 470-495, EM 510-550, DM 505 (bandpass)
Olympus U-MNB2: EX 470-490, EM 520IF, DM 500 (longpass)
Olympus U-MNIGA3: EX 540-550, EM 575-625, DM 570 (bandpass)
Olympus U-NA49006: EX 620/60, EM 700/75, DM DC660LP (longpass)

Transmitted Light:

Brightfield

Camera:

Olympus DP30BW Microscope Digital Camera (monochrome)

Software:

DP Controller (2.2.1.227) + DP Manager (2.2.1.195)

Zeiss Axio Scope.A1 Upright Fluorescence Microscope

Zeiss Axio Scope.A1

Zeiss Axio Scope.A1 with Zeiss Axiocam 506 color camera for large sample areas with high resolution making subtle color differences visible in great quality. Photo: Outi Paloheimo/University of Tampere

Widefield fluorescence microscope for fixed samples. Compact system with a large range of features. Equipped high-quality color camera with the large field of view and number of pixels (2752 horizontal pixels × 2208 vertical pixels). Axiocam 506 color offers a dynamic range of 1:2500 for optimized color reproduction.

Features:

Zeiss Axio Scope.A1 upright microscope
Specimen holder for sliders 76×26 mm

Objectives:

Zeiss N-Achroplan 5x/0.15, WD 12.0 mm (Air)
Zeiss Plan-Apochromat Ph 1 10x/0.45, WD 2.1 mm (Air)
Zeiss LD Plan-Apochromat Ph 2 20x/0.80, WD 0.55 mm Air)
Zeiss LD Plan-Apochromat Corr Ph 3 40x/0.95, WD 0.25 mm (Air)
Zeiss Plan-Apochromat Ph3 63x/1.40, WD 0.19 mm (Oil)
Zeiss Plan-Neofluar 100x/1.30, WD 0.20 mm (Oil)

Light sources and filters:

Epifluorescence Illuminator HXP 200 C in combination with HAL 100 transmitted-light

Zeiss Filter set 49: EX G 365, BS FT 395, EM BP 445/50
Zeiss Filter set 38: EX BP 470/40, BS FT 495, EM BP 525/50
Zeiss Filter set 20: EX BP 546/12, BS FT 560, EM BP 575-640
Zeiss Filter set 50: EX BP 640/30, BS FT 660, EM BP 690/50

Transmitted Light:

Brightfield
Phase Contrast
Darkfield
DIC

Camera:

Zeiss Axiocam 506 color

Software:

ZEN pro 2011

Microscopes for Electrophysiological Research

Nikon Eclipse FN1 Upright Fluorescence Microscope

Nikon Eclipse FN1

Nikon Eclipse FN1 is a special fixed stage upright microscope that has optical system including water dipping objective with depth-induced aberration correction. Photo: Outi Paloheimo/University of Tampere

The FN1 fluorescence microscope is optimized for fluorescence microscopy of living specimens. It is equipped with micromanipulation and patch clamp possibility.

Features:

Dipping objectives
16 LED fluorescence light source
DIC
IR-DIC
Reflection imaging
Extra zoom unit (0.6x-2.0x)
Objective and sample stage heaters

Objectives:

Nikon CFI Plan Fluor 10x/0.3, WD 3.5 mm, water dipping
Nikon CFI Fluor 40x/0.8, WD 2.0 mm, water dipping
Nikon CFI Apo LWD 25x/1.1, WD 2.0 mm, water dipping 

Light source:

CoolLED pE-4000

Transmitted Light:

Brightfield
DIC
IR-DIC

Camera:

Hamamatsu Orca-Flash4.0 V2 CMOS camera

Software:

NIS-Elements D

Image Processing

Image Analysis Computers

Analysis computers

Tampere Imaging Facility offers two analysis computers for image processing in dedicated offices. Photo: Outi Paloheimo/University of Tampere

Tampere Imaging Facility offers two analysis computers for image processing in dedicated offices. One is specially meant for deconvolution and equipped with software of Scientific Volume Imaging (Huygens Essential). The other is specially meant for image processing of data acquired with our cell observation incubators CM Technologies Cell-IQ® and Nikon BioStation CT (timelapse imaging systems).

Image Analysis Deconvolution and interactive pen display:

AGM Titan Xp i7
Processor: CPU – Intel Core i7 6900K 3,7GHz LGA 2011-v3
Memory: RAM – Corsair 64 GB (3200 MHz DDR4), 4 x 8GB
Graphics Card: GPU – Titan Xp

Scientific Volume Imaging Huygens Essential

Huygens Essential is tailored for deconvolution and processing of microscopy images. Its wizard-driven user interface guides you through the process of deconvolving microscopy images.

Wacom Cintiq® 22HD interactive pen display

Enables creating directly on a large high-definition display with Wacom’s pressure-sensitive pen. Compatible with several of softwares like ImageJ, Adobe Illustrator, and Adobe Photoshop.

NIS-Elements Advanced Research Microscope Imaging Software

Nikon’s powerful software for visualization, data management and analysis. Offers many image processing features and handles large data sets.

Adobe Creative Cloud

Including Photoshop, Illustrator, InDesign, Premiere Pro, and more.

Other available softwares:

BioImageXD
Blender
CellProfiler
ImageJ
Inkscape
Vaa3D
Voxx2
ZEN lite

Image Analysis Cell-IQ and BioStation:

Dell Precision Tower 5810 XCTO Base
Processor: Intel Xeon Processor E5-1660 v3 (8C HT, 20MB Cache, 3.0 GHz Turbo)
Memory: 64GB (4x16GB) 2400MHz DDR4 RDIMM ECC

Cell-IQ®Analyser (Version MA4.3.0.0)

In CM Technologies Cell-IQ samples are monitored via the Imagen™ program, and the Analyser™ software automates the process of quantitation measuring multiple cellular parameters from phase contrast and fluorescence images.

Nikon CL-Quant (Version 3.10)

CL-Quant is image analysis software that features an automatic cell identification functions of data obtained via Nikon BioStation CT. It can automatically identify cell regions in phase contrast or epifluorescence images using algorithms.

Other available softwares:

Adobe Creative Cloud (including Photoshop, Illustrator, InDesign, Premiere Pro, and more)
ImageJ
NIS Elements Viewer
ZEN lite

Prices

SYSTEM RESERVATION: COMPUTERS PRICE/HOUR
Image Analysis computer for processing of Cell-IQ® and BioStation data
(Agendo name: Image Analysis Cell-IQ and BioStation)
0,00 €
Image Analysis computer for deconvolution and other image processing
(Agendo name: Image Analysis Deconvolution and interactive pen display)
0,00 €
SYSTEM RESERVATION: CONFOCAL MICROSCOPES PRICE/HOUR
Nikon A1R+ laser scanning confocal microscope
(Agendo name: Nikon A1R with N-SIM)
22,00 €
Nikon Spinning Disk laser scanning confocal microscope
(Agendo name: Nikon Spinning Disk)
10,00 €
Zeiss LSM 700 laser scanning confocal microscope
(Agendo name: Zeiss LSM 700 LSCM)
12,00 €
Zeiss LSM 780 laser scanning confocal microscope
(Agendo name: Zeiss LSM 780 LSCM)
20,00 €
SYSTEM RESERVATION: SUPER-RESOLUTION MICROSCOPES PRICE/HOUR
Nikon N-SIM Super-Resolution Microscope System
(Agendo name: Nikon A1R with N-SIM)
22,00 €
SYSTEM RESERVATION: TIMELAPSE IMAGING PRICE/HOUR
CM Technologies Cell-IQ® automated imaging and analysis system
(Agendo name: CM Technologies Cell-IQ slot 1)
0,85 €
Nikon BioStation CT observation incubator for automated imaging and analysis
(Agendo name: Nikon BioStation CT slots 1-5)
0,85 €
SYSTEM RESERVATION: WIDEFIELD FLUORESCENCE MICROSCOPES – ADVANCED PRICE/HOUR
Nikon Eclipse FN1 upright fluorescence microscope for electrophysiological research
(Agendo name: Nikon FN1 Upright Fluorescence Microscope)
8,00 €
Zeiss ApoTome.2 upright fluorescence microscope using structured illumination
(Agendo name: Zeiss ApoTome.2 Fluorescence Microscope)
7,00 €
SYSTEM RESERVATION: WIDEFIELD FLUORESCENCE MICROSCOPES – BASIC PRICE/HOUR
Olympus IX51 inverted fluorescence microscope
(Agendo name: Olympus IX51 Fluorescence Microscope)
1,00 €
Zeiss Axio Scope.A1 upright fluorescence microscope
(Agendo name: Zeiss Axio Scope.A1 Fluorescence Microscope)
1,00 €
SYSTEM RESERVATION: WIDEFIELD FLUORESCENCE MICROSCOPES – SPECIAL PRICE/HOUR
Nikon AZ100 multizoom upright fluorescence macroscope
(Agendo name: Nikon AZ100 Fluorescence Macroscope)
2,00 €
Olympus BX61WI upright water immersion fluorescence microscope (Note: Currently not in use!)
(Agendo name: Olympus BX61WI Water Immersion Fluorescence Microscope)
1,00 €

Pricing is valid for user groups from University of Tampere and Tampere University of Technology. Other academic or non-academic users are asked to inquire specific pricing.

Prices above are applicable from Monday to Friday 8 am to 4 pm. Discount of 50 % is applied for reservations on night time between 4 pm to 8 am and on weekends.

Tampere Imaging Facility reserves the right to price adjustments.

ACKNOWLEDGEMENT

All the users of Tampere Imaging Facility (TIF) services are obligated to acknowledge the facility in publications:

“The authors acknowledge Tampere Imaging Facility (TIF) for their service.”

Contacts

Imaging Systems:

Support’s shared email address:
COFAmicroscopy(at)uta.fi

Reservations, equipment details:

Outi Paloheimo, M.Sc.
Tel: +358 50 318 6766
Room: ARVO D436

Scientific Advisor:

Teemu Ihalainen, Ph.D., Adj. Prof.
Tel: +358 50 518 7422
Room: ARVO D264

Management:

Susanna Narkilahti, Ph.D., Adj. Prof.
Tel: +358 40 708 5113
Room: ARVO D428

Tampere Imaging Facility Publications

2017

Kumar M, Rahikainen R, Unruh D, Hytönen VP, Delbrück C, Sindelar R, Renz F.
Mixture of PLA-PEG and biotinylated albumin enables immobilization of avidins on electrospun fibers.
J Biomed Mater Res A. 2017 Feb;105(2):356-362. doi: 10.1002/jbm.a.35920. Epub 2016 Oct 21. PMID: 27684712

Kreutzer J, Ylä-Outinen L, Mäki AJ, Ristola M, Narkilahti S, Kallio P.
Cell culture chamber with gas supply for prolonged recording of human neuronal cells on microelectrode array.
J Neurosci Methods. 2017 Mar 15;280:27-35. doi: 10.1016/j.jneumeth.2017.01.019. Epub 2017 Feb 1. PMID: 28161299

Koivisto JT, Joki T, Parraga JE, Pääkkönen R, Ylä-Outinen L, Salonen L, Jönkkäri I, Peltola M, Ihalainen TO, Narkilahti S, Kellomäki M.
Bioamine-crosslinked gellan gum hydrogel for neural tissue engineering.
Biomed Mater. 2017 Mar 24;12(2):025014. doi: 10.1088/1748-605X/aa62b0. PMID: 28233757

Calejo MT, Ilmarinen T, Vuorimaa-Laukkanen E, Talvitie E, Hakola HM, Skottman H, Kellomäki M.
Langmuir-Schaefer film deposition onto honeycomb porous films for retinal tissue engineering.
Acta Biomater. 2017 May;54:138-149. doi: 10.1016/j.actbio.2017.02.035. Epub 2017 Feb 20. PMID: 28223209

Oksala NKJ, Seppälä I, Rahikainen R, Mäkelä KM, Raitoharju E, Illig T, Klopp N, Kholova I, Laaksonen R, Karhunen PJ, Hytönen VP, Lehtimäki T.
Synergistic Expression of Histone Deacetylase 9 and Matrix Metalloproteinase 12 in M4 Macrophages in Advanced Carotid Plaques.
Eur J Vasc Endovasc Surg. 2017 May;53(5):632-640. doi: 10.1016/j.ejvs.2017.02.014. Epub 2017 Mar 23. PMID: 28343758

Leivo J, Virjula S, Vanhatupa S, Kartasalo K, Kreutzer J, Miettinen S, Kallio P.
A durable and biocompatible ascorbic acid-based covalent coating method of polydimethylsiloxane for dynamic cell culture.
J R Soc Interface. 2017 Jul;14(132). pii: 20170318. doi: 10.1098/rsif.2017.0318. PMID: 28747398

Virjula S, Zhao F, Leivo J, Vanhatupa S, Kreutzer J, Vaughan TJ, Honkala AM, Viehrig M, Mullen CA, Kallio P, McNamara LM, Miettinen S.
The effect of equiaxial stretching on the osteogenic differentiation and mechanical properties of human adipose stem cells.
J Mech Behav Biomed Mater. 2017 Aug;72:38-48. doi: 10.1016/j.jmbbm.2017.04.016. Epub 2017 Apr 13. PMID: 28448920

Hyysalo A, Ristola M, Joki T, Honkanen M, Vippola M, Narkilahti S. Aligned Poly(ε-caprolactone) Nanofibers Guide the Orientation and Migration of Human Pluripotent Stem Cell-Derived Neurons, Astrocytes, and Oligodendrocyte Precursor Cells In Vitro.
Macromol Biosci. 2017 Jul;17(7). doi: 10.1002/mabi.201600517. Epub 2017 Mar 15. PMID: 28296144

Turunen S, Joki T, Hiltunen ML, Ihalainen TO, Narkilahti S, Kellomäki M.
Direct Laser Writing of Tubular Microtowers for 3D Culture of Human Pluripotent Stem Cell-Derived Neuronal Cells.
ACS Appl Mater Interfaces. 2017 Aug 9;9(31):25717-25730. doi: 10.1021/acsami.7b05536. Epub 2017 Jul 31. PMID: 28697300

Skottman H, Muranen J, Lähdekorpi H, Pajula E, Mäkelä K, Koivusalo L, Koistinen A, Uusitalo H, Kaarniranta K, Juuti-Uusitalo K.
Contacting co-culture of human retinal microvascular endothelial cells alters barrier function of human embryonic stem cell derived retinal pigment epithelial cells.
Exp Cell Res. 2017 Aug 8. pii: S0014-4827(17)30415-9. doi: 10.1016/j.yexcr.2017.08.004. [Epub ahead of print] PMID: 28800962

Kiamehr M, Viiri LE, Vihervaara T, Koistinen KM, Hilvo M, Ekroos K, Käkelä R, Aalto-Setälä K.
Lipidomic profiling of patient-specific iPSC-derived hepatocyte-like cells.
Dis Model Mech. 2017 Sep 1;10(9):1141-1153. doi: 10.1242/dmm.030841. Epub 2017 Jul 21. PMID: 28733363

Hyysalo A, Ristola M, Mäkinen ME, Häyrynen S, Nykter M, Narkilahti S.
Laminin α5 substrates promote survival, network formation and functional development of human pluripotent stem cell-derived neurons in vitro.
Stem Cell Res. 2017 Sep 12;24:118-127. doi: 10.1016/j.scr.2017.09.002. [Epub ahead of print] PMID: 28926760

2016

Kemppainen E, George J, Garipler G, Tuomela T, Kiviranta E, Soga T, Dunn CD, Jacobs HT.
Mitochondrial Dysfunction Plus High-Sugar Diet Provokes a Metabolic Crisis That Inhibits Growth.
PLoS One. 2016 Jan 26;11(1):e0145836. doi: 10.1371/journal.pone.0145836. eCollection 2016. Erratum in: PLoS One. 2016;11(3):e0151421. PMID: 26812173

Vuornos K, Björninen M, Talvitie E, Paakinaho K, Kellomäki M, Huhtala H, Miettinen S, Seppänen-Kaijansinkko R, Haimi S.
Human Adipose Stem Cells Differentiated on Braided Polylactide Scaffolds Is a Potential Approach for Tendon Tissue Engineering.
Tissue Eng Part A. 2016 Mar;22(5-6):513-23. doi: 10.1089/ten.tea.2015.0276. Epub 2016 Feb 26. PMID: 26919401

Calejo MT, Ilmarinen T, Jongprasitkul H, Skottman H, Kellomäki M.
Honeycomb porous films as permeable scaffold materials for human embryonic stem cell-derived retinal pigment epithelium.
J Biomed Mater Res A. 2016 Jul;104(7):1646-56. doi: 10.1002/jbm.a.35690. Epub 2016 Mar 15. PMID: 26914698

Anderl I, Vesala L, Ihalainen TO, Vanha-Aho LM, Andó I, Rämet M, Hultmark D.
Transdifferentiation and Proliferation in Two Distinct Hemocyte Lineages in Drosophila melanogaster Larvae after Wasp Infection.
PLoS Pathog. 2016 Jul 14;12(7):e1005746. doi: 10.1371/journal.ppat.1005746. eCollection 2016 Jul. PMID: 27414410

Hynninen V, Vuori L, Hannula M, Tapio K, Lahtonen K, Isoniemi T, Lehtonen E, Hirsimäki M, Toppari JJ, Valden M, Hytönen VP.
Improved antifouling properties and selective biofunctionalization of stainless steel by employing heterobifunctional silane-polyethylene glycol overlayers and avidin-biotin technology.
Sci Rep. 2016 Jul 6;6:29324. doi: 10.1038/srep29324. PMID: 27381834

Lenk K, Priwitzer B, Ylä-Outinen L, Tietz LH, Narkilahti S, Hyttinen JA.
Simulation of developing human neuronal cell networks.
Biomed Eng Online. 2016 Aug 30;15(1):105. doi: 10.1186/s12938-016-0226-6. PMID: 27576323

Andjelković A, Kemppainen KK, Jacobs HT.
Ligand-Bound GeneSwitch Causes Developmental Aberrations in Drosophila that Are Alleviated by the Alternative Oxidase.
G3 (Bethesda). 2016 Sep 8;6(9):2839-46. doi: 10.1534/g3.116.030882. PMID: 27412986

von Essen M, Rahikainen R, Oksala N, Raitoharju E, Seppälä I, Mennander A, Sioris T, Kholová I, Klopp N, Illig T, Karhunen PJ, Kähönen M, Lehtimäki T, Hytönen VP.
Talin and vinculin are downregulated in atherosclerotic plaque; Tampere Vascular Study.
Atherosclerosis. 2016 Dec;255:43-53. doi: 10.1016/j.atherosclerosis.2016.10.031. Epub 2016 Oct 15. PMID: 27816808

2015

Faia-Torres AB, Goren T, Ihalainen TO, Guimond-Lischer S, Charnley M, Rottmar M, Maniura-Weber K, Spencer ND, Reis RL, Textor M, Neves NM.
Regulation of human mesenchymal stem cell osteogenesis by specific surface density of fibronectin: a gradient study.
ACS Appl Mater Interfaces. 2015 Feb 4;7(4):2367-75. doi: 10.1021/am506951c. Epub 2015 Jan 23. PMID: 25513839

Vanha-Aho LM, Anderl I, Vesala L, Hultmark D, Valanne S, Rämet M.
Edin Expression in the Fat Body Is Required in the Defense Against Parasitic Wasps in Drosophila melanogaster.
PLoS Pathog. 2015 May 12;11(5):e1004895. doi: 10.1371/journal.ppat.1004895. eCollection 2015 May. PMID: 25965263

Ribeiro C, Pärssinen J, Sencadas V, Correia V, Miettinen S, Hytönen VP, Lanceros-Méndez S.
Dynamic piezoelectric stimulation enhances osteogenic differentiation of human adipose stem cells.
J Biomed Mater Res A. 2015 Jun;103(6):2172-5. doi: 10.1002/jbm.a.35368. Epub 2014 Nov 11. PMID: 25370596

Syrjänen L, Valanne S, Kuuslahti M, Tuomela T, Sriram A, Sanz A, Jacobs HT, Rämet M, Parkkila S.
β carbonic anhydrase is required for female fertility in Drosophila melanogaster.
Front Zool. 2015 Aug 22;12:19. doi: 10.1186/s12983-015-0111-3. eCollection 2015. PMID: 26300950 Free PMC Article

Oksala N, Pärssinen J, Seppälä I, Klopp N, Illig T, Laaksonen R, Levula M, Raitoharju E, Kholova I, Sioris T, Kähönen M, Lehtimäki T, Hytönen VP.
Kindlin 3 (FERMT3) is associated with unstable atherosclerotic plaques, anti-inflammatory type II macrophages and upregulation of beta-2 integrins in all major arterial beds.
Atherosclerosis. 2015 Sep;242(1):145-54. doi: 10.1016/j.atherosclerosis.2015.06.058. Epub 2015 Jul 13. PMID: 26188538

Koho T, Ihalainen TO, Stark M, Uusi-Kerttula H, Wieneke R, Rahikainen R, Blazevic V, Marjomäki V, Tampé R, Kulomaa MS, Hytönen VP.
His-tagged norovirus-like particles: A versatile platform for cellular delivery and surface display.
Eur J Pharm Biopharm. 2015 Oct;96:22-31. doi: 10.1016/j.ejpb.2015.07.002. Epub 2015 Jul 10. PMID: 26170162

Ihalainen TO, Aires L, Herzog FA, Schwartlander R, Moeller J, Vogel V.
Differential basal-to-apical accessibility of lamin A/C epitopes in the nuclear lamina regulated by changes in cytoskeletal tension.
Nat Mater. 2015 Dec;14(12):1252-61. doi: 10.1038/nmat4389. Epub 2015 Aug 24. PMID: 26301768

2014

Rajala N, Gerhold JM, Martinsson P, Klymov A, Spelbrink JN.
Replication factors transiently associate with mtDNA at the mitochondrial inner membrane to facilitate replication.
Nucleic Acids Res. 2014 Jan;42(2):952-67. doi: 10.1093/nar/gkt988. Epub 2013 Oct 25. PMID: 24163258

Kemppainen KK, Rinne J, Sriram A, Lakanmaa M, Zeb A, Tuomela T, Popplestone A, Singh S, Sanz A, Rustin P, Jacobs HT.
Expression of alternative oxidase in Drosophila ameliorates diverse phenotypes due to cytochrome oxidase deficiency.
Hum Mol Genet. 2014 Apr 15;23(8):2078-93. doi: 10.1093/hmg/ddt601. Epub 2013 Nov 29. PMID: 24293544

Vartiainen S, Chen S, George J, Tuomela T, Luoto KR, O’Dell KM, Jacobs HT.
Phenotypic rescue of a Drosophila model of mitochondrial ANT1 disease.
Dis Model Mech. 2014 Jun;7(6):635-48. doi: 10.1242/dmm.016527. Epub 2014 May 8. PMID: 24812436

Fukuoh A, Cannino G, Gerards M, Buckley S, Kazancioglu S, Scialo F, Lihavainen E, Ribeiro A, Dufour E, Jacobs HT.
Screen for mitochondrial DNA copy number maintenance genes reveals essential role for ATP synthase.
Mol Syst Biol. 2014 Jun 21;10:734. doi: 10.15252/msb.20145117. PMID: 24952591

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