BioMediTech Research Infrastructure

Histology Facility

Histology facility (HF) welcomes all researchers from MED and TUT to do their tissue histology work using the modern histotechnology equipment  and microscopes. Our technicians will help you with technical issues and can do the tissue processing, staining and analysis whenever possible. HF encourages to use digital microscope and whole slide scanning to generate material for your quantitative scientific analyses.


Histology Facility (HF) is located in the Arvo building, 3rd floor (E-wing, laboratories and microscope rooms). Researchers can use the laboratory equipment and microscopes themselves (with guidance by the HF lab technicians) or ask for the availability of turnkey services done by the HF staff. See description below.

Tissue technologies:

HF has two tissue processors for preparing paraffin blocks of solid tissue samples. Both formalin-fixed and Paxgene-fixed tissues can be prepared.

HF has several rotary and sliding microtomes for cutting paraffin blocks (section thickness adjustable to 2-6um). For cutting frozen sections several Leica and Microm cryomicrotomes are available.

Cultured cells in suspension can be prepared as sectionable tissue blocks using the thrombin clotting technique. Alternatively, Sakura Cytocentrifuge can be used to prepare cell slides for IHC and IF staining.

HF has two Kedee stainers for automated hematoxylin-eosin and other routine stains. Slide coverslipping can be done automatically using DAKO coverslipper.

HF has two Ventana BenchMark and three LabVision autostainers for automated immunohistochemistry. Antigen retrieval can be done with a PT Module, Retriever 2100, or a microwave oven using ph6 or pH9 buffers.

Immunofluorescence staining can be done using LabVision Autostainer or manually using various staining racks available. Of these, JL-Stainer is well-suited for staining of 1-10 IF slides.

For in situ hybridization, HF has a fully automated PathCom stainer, which allows IHC, mRNA in situ and DNA in situ hybridization (both CISH and FISH). PathCom has built-in deparaffinization, antigen retrieval as well as proteolytic digestion. mRNA in situ has been done using the RNAscope protocol and reagents.

Tissue microarray paraffin blocks can be prepared using the 3D Histech TMA Master. 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.

HF has several Olympus BX and Leica DM microscope for slide inspection. Some of these are equipped with digital cameras for snapshot imaging.

HF has a Zeiss Axioplan microscope for multicolor fluorescence imaging and image capture. The microscope is equipped with ApoTome device, which allows structured illumination principle for generating sharp sections-within-section confocal-type images with all wavelengths. The microscope is operated with AxioVision software.

HF has a QIAGEN Qiacube device for extraction of DNA or RNA from frozen or paraffin block tissue sections. For paraffin block RNA extraction, PAXgene tissue fixation is recommended.

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

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.

See our website for basic introduction.

Virtual slide scanning systems

HF has two virtual slide scanners, (SlideStrider, Jilab, Finland), which enable scanning of up to 200 microscope slides in one batch. Alternatively, scanning of 2×3 inch macroslides is also possible. Scanning resolutions 0.31 um/pixel (using 10X lens) and 0.16 um/pixel (using 20X lens) can be selected by the user. Scanning with oil immersion lenses is also possible.

Both scanners allow scanning with epifluorescence illumination using blue, green and red emission wavelenghts. The scanning output image format is jpeg2000. The viewing software for virtual slides can be downloaded from our website.

Virtual microscopy scanning system for microwell plates

Microwell plates can be scanned using a scanning system mounted in an inverted microscope (Olympus IX71) or using EVOS FL Auto. These systems allow 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.


All the users of the Histology Facility (HF) services are obligated to acknowledge the facility in publications:

“The authors acknowledge the Tampere Histology Facility (HF) for their service.”


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


Laboratory technician:
Sari Toivola
Tel: +358 40 190 4071

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