Microscopy and Histology

  • Introduction
  • Equipment
  • Prices
  • Contacts

Tampere Imaging Facility (TIF) is situated in BioMediTech (BMT), University of Tampere (UTA). It offers state-of-the-art imaging systems for life- and material scientists. TIF includes spinning disk confocal microscope for high-resolution microscopy of living samples, laser scanning confocal system for living and fixed samples, structured illumination systems for non-confocal optical sectioning, long timelapse imaging systems, widefield systems for live and fixed cells and high-throughput systems (Virtual Microscopy platform) for fixed samples (tissue sections). TIF also has data processing and analysis stations available with deconvolution, visualization and image quantification possibilities.

In addition to the microscopy services, the facility provides automated equipment for paraffin-block tissue processing (cultured cells can be processed as paraffin blocks using thrombin-clotting technology), tissue microarray (TMA) preparation, microtomy and hematoxylin and eosin staining. Immunohistochemistry is carried out by using automated staining. Cryomicrotome for preparing frozen sections is also available. For molecular biology purposes DNA and RNA can be extracted from tissue blocks.

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

Useful links:

Booking system for the microscopes (works with Firefox, Chrome and Safari)

You can view more detailed information (e.g. objectives, filters, and detectors) by clicking blue
equipment names, such as Andor spinning disk. The second click will hide the details again.

Microscopy Systems

Confocal Microscopes

    Andor spinning disk (Yokogawa CSU10)

    Confocal imaging system for living cells/samples. Equipped with incubation, hardware based autofocus and FRAP/FLIP/photoactivation unit for studies of protein dynamics.


    • Nikon Eclipse-Ti microscope (inverted microscope) with "Perfect Focus System ®" -autofocus
    • Stage-top incubator with heating and CO2
    • Morotized stage from Prior allowing multipoint imaging
    • FRAPPA-unit for photobleaching and –activation studies
    • Objectives:
    • Plan-Apochromat 100x/1.4 (oil)
    • Plan-Apochromat 40x/1.0 (oil)
    • Plan-Apochromat 40x/1.15 (water) corr, > 500 µm WD!
    • Plan-Apochromat 20x/0.5
    • Plan-Apochromat 10x/0.3
    • Lasers and filters:
    • DPSS-Lasers: 405 nm, 488 nm, 561 nm and 640 nm
    • 6 different emission filters for the commonly used fluorophores and fluorescent proteins
    • Detector/camera:
    • Andor Neo sCMOS camera

    Zeiss LSM780 Laser Scanning Confocal Microscope

    LSCM for living and fixed samples. Equipped with large incubator, 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 Correalation Spectoscopy (FCS), FRAP/FLIP/Photoactivation possibility.


    • Zeiss Cell Obserer.Z1 microscope (inverted microscope)
    • Large incubator with heating and CO2 control
    • Motorized stage for multipoint imaging
    • Fluorescence Correlation Spectroscopy (FCS) possibility
    • Tunable pulsed laser
    • Objectives:
    • Plan Apochromat 63x/1.4 (oil)
    • Plan Apochromat 63x/1.2 (water) Corr
    • Plan-Apochromat 40x/1.4 (oil)
    • Plan-Apochromat 20x/0.8
    • Plan-Apochromat 10x/0.45
    • Lasers and filters:
    • Pulsed diode laser 405 nm, multiline Argon laser: 456 nm, 488 nm, 514 nm, diode laser 561 nm, HeNe-lasers: 594 nm and 633 nm
    • InTune-tunable pulsed laser: 490 nm – 640 nm
    • Detector/camera:
    • Quasar spectral GaAsP PMT array allowing fast spectral imaging

Structured Illumination Microscopes

    Zeiss Apotome

    Widefield fluorescence microscope equipped with Apotome structured illumination system allowing optical sectioning. The system can be used also as a standard widefield epifluorescence microscope and it’s suitable mainly for fixed or stationary samples.


    • AxioImager.M2 (upright microscope)
    • Manual stage
    • Objectives:
    • EC Plan Neofluar 63x/1.25 (oil)
    • Plan Neofluar 40x/1.3 (oil)
    • EC Plan Neofluar 10x/0.3
    • Filters (suitable dyes or spectrally equal dyes):
    • Zeiss Filter Set 49: single filter for Dapi
    • Zeiss Filter Set 38: single filter for EGFP
    • Zeiss Filter Set 20: single filter for TRITC
    • Detector/camera:
    • Zeiss Axiocam MRm CCD camera

    Zeiss Apotome.2

    Widefield fluorescence microscope equipped with second generation Apotome.2 structured illumination system. It has variety of possible excitation wavelengths (LED based), emission filters and objectives and can be used also as a widefield epifluorescence microscope. It’s suitable mainly for fixed or stationary samples.


    • AxioImager.M2 (upright microscope)
    • Motorized stage
    • Objectives:
    • EC Plan Neofluar 100x/1.3 (oil)
    • EC Plan Neofluar 40x/0.75
    • EC Plan Neofluar 20x/0.5
    • EC Plan Neofluar 10x/0.3
    • EC Plan Neofluar 5x/0.16
    • EC Plan Neofluar 2.5x/0.075
    • Light sources and filters:
    • Colibri LED light source (380 nm, 420 nm, 470 nm, 505 nm, 555 nm, 590 nm and 625 nm LED).
    • Filters (suitable dyes or spectrally equal dyes):
    • Zeiss Filter Set 62: triple filter for Dapi/EGFP/mCherry
    • Zeiss Filter Set 56: dual filter for EGFP/TRITC
    • Zeiss Filter Set 50: single filter for Cy5
    • Zeiss Filter Set 46: single filter for EYFP
    • Zeiss Filter Set 38: single filter for EGFP
    • Zeiss Filter Set 05: single filter for ECFP (wide emission band)
    • Detector/camera:
    • Zeiss Axiocam HRm CCD camera

Timelapse Imaging Systems

    Chipman CellIQ

    Live cell imaging system with stable incubation for long timelapse imaging


    • Easy to use software for programming imaging cycles
    • Incubator with heating and CO2
    • Autofocus and Z-stack possibility
    • Capacity up to 2 well plates/flasks simultaneously
    • Objectives:
    • Nikon S Plan Fluor ELWD 40x/0.60
    • Nikon S Plan Fluor ELWD 20x/0.45
    • Nikon Plan Fluor 10x/0.30
    • Nikon Plan Fluor 4x/0.13
    • Light sources and filters:
    • PE Excitation system with LED light source (470 nm, 550 nm, 660 nm)
    • Semrock Filter set LF488/LP-B-L01 for EGFP (long pass filter)
    • Semrock Filter set LF561/LP-A-L01 for mCherry (long pass filter)
    • Semrock Filter set Cy5.5-B-L01 for Cy5.5 (bandpass 690 nm – 740 nm)
    • Detector/camera:
    • Retiga EXi 1392 CCD camera

    Nikon Biostation CT

    Live cell imaging system with incubation for long timelapse imaging


    • Easy to use software for programming imaging cycles
    • Incubator with controlled humidity and CO2 environment integrated with CCD camera and microscope
    • Robotic arm transfers cell plates to microscope from holder racks
    • Active auto-focus for long-term timelapse imaging
    • Capacity up to 30 well plates/flasks simultaneously
    • Objectives:
    • Magnifications 2-40X
    • Light sources and filters:
    • BS-FL Fluorescence Unit
    • T-FL-E Motorized Epi-Fl Filter Cube Holder CT
    • C-FL Epi-Fl Filter Cube Cy5 for BS-CT
    • C-FL Epi-Fl Filter Cube GFP for BS-CT
    • C-FL Epi-Fl Filter Cube TxRed for BS-CT
    • Detector/camera:
    • CCD camera

Conventional brightfield microscopes

    IBT has in use several brightfield microscopes equipped with digital color CCD cameras. Standard upright microscopes with 2X-100X objectives can be used for imaging of stained tissue sections and coverslipped monolayer cell cultures.

Conventional widefield epifluorescence microscopes

    Several brightfield microscopes are equipped with epifluorescence illumination equipment, allowing inspection and imaging of fluorescent samples. Magnifications matching 5X-100X objective lenses are available.

Image processing

    Dell Precision T3600

      Intel Xeon Processor E5-2665 (8 Core, 2.40GHz Turbo)
      Memory: 16GB (4x4GB) 1600MHz DDR3

      Available softwares:
      Huygens Essential deconvolution


Laser capture microdissection

    Veritas Arcturus Laser Capture microdissection system is available for isolation of cell islets and single cells from cultures and frozen tissue sections. The dissected material can be studied with molecular biology methods (e.g. PCR-based).

Tissue technologies

    LabVision Autostainer technology is available for automated immunohistochemistry.

    3D Histech’s TMA Master can be used in the tissue microarray (TMA) block preparation. The system allows preparation of 0.6-2 mm diameter tissue cores punched and inserted in 1-2 recipient TMA blocks. Sectioning and staining of TMA blocks follows the principles of conventional tissue samples.

    QIAGEN systems for DNA and RNA extraction from tissue blocks

    Sakura Cytocentrifuge can be used to spun cell suspensions on to microscope objective slides

Virtual Microscopy

Virtual microscopy stands for acquiring and handling digitized versions of microscope glass slides, which are in turn commonly referred to as "virtual slides" or "whole-slide images" (WSIs). Virtual slides are montage images consisting of up to thousands of high resolution digital micrographs (image tiles).

See our website http://jvsmicroscope.uta.fi for basic introduction.

Virtual slide scanning systems

    TIF has virtual slide scanning system, which is based on an upright microscope (Zeiss Axioskop), a motorized specimen stage for 8 slides (or 4 macroslides). This system enables scanning using any microscope objective (5X-100X), including oil immersion lenses.

    This system includes also epifluorescence illumination with a motorized filter changer. Thus, the system allows multichannel fluorescence scanning. The scanning output type (bmp, tif, jpeg2000) can be selected by the user. The viewing software for virtual slides is available from our website.

    In collaboration with TAUH (Centre for Laboratory Medicine) we have access to a high-throughput scanner (Aperio Scanscope XT), which allows scanning daily of 120 slides at 20X objective magnification. The output files are processed as JPEG2000.

Virtual microscopy scanning system for microwell plates

    Microwell plates can be scanned using a scanning system mounted in an inverted microscope (Olympus IX71). The hardware (from Objective Imaging Inc) is similar to that in the upright microscope scanner (see above). This system allows scanning of cells grown on Petri dishes and 24-96 well microplates. The basic illumination system is phase contrast but fluorescent illumination (with motorized filter changer) is also possible.

Prices will be defined based on customer needs. Please inquire!

Imaging Systems:

Support's shared email address:

Imaging Specialist
Teemu Ihalainen, Ph.D.
Tel: +358 50 518 7422
Room: ARVO D436

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

Histology and virtual microscopy:

Jorma Isola
Tel: +358 50 318 3196
Room: ARVO D239