BI Histoscanner

Scan all of your samples on our digital slide scanner and use your computer as your microscope!

We provide high-throughput, brightfield scanning (with 20X and 40X air objectives) for your microscopy slides. Located at the Institute of Biotechnology (HiLIFE Unit, Viikki), we will efficiently scan your slides and you can retrieve the files from our university server to be viewed at your convenience on any computer. This service allows easy, fast, and high-quality analysis of digitized slides and is excellent for presentations and publications.

Beforehand, tissue embedding, sectioning, staining, and mounting on slides can be easily performed in our Histology Core Facility.


Before bringing your slides, please use this form to submit scanning orders.

Drop off Address: Institute of Biotechnology, Histoscanner, BIOKESKUS 2 (Viikinkaari 5D), room 5032A (5th floor),  00014 University of Helsinki

If you have any questions, please do not hesitate to contact us.

Contact Email:


Our services are open to both academic and commercial users.

List of services and fees (effective 01/01/2022).

  University of Helsinki Commercial
Price of scanning (per slide):    
20x Single layer 5 € 15 €
40x Single layer 7 € 20 €
20x Extended Focus or Z-stack 7 € 20 €
40x Extended Focus or Z-stack 10 € 25 €
20x/40x scanning >1 hour (e.g., extended focus, Z-stack) 12 € 50 €
Price of compression and upload to Aiforia (per set):    
11-100 slides, single focus 12 € 12 €
11-100 slides, extended focus 25 € 25 €
Price of manual scanning (per 30 min): 25 € 80 €
Preparing your slides
  • Slide must be between 0,9 mm and 1,2 mm thick
  • Sections should be close to the centre of the slide (> 5mm)
  • Fewer sections per slide than normally
  • Mounted with permanent mounting media and let dry at least 24 hours
  • Place coverslip carefully. Coverslip must not protrude over the edge of the slide at all
  • Slides should be cleaned of excess mounting media
  • No broken slides or coverslips
  • If you wish to have your slide files named, you may include an excel file with the names of the slides in the exact order in which you have given them
  • Average file size is 1-1,5 GB
  • You can transfer your data from our server, but only for temporary storage
  • Install free Digital Slide Viewer softwares from 3DHISTECH
  • Aiforia® : If you wish to upload files to Aiforia®, you must provide a list of slide names with the slides
Scanner and image information
  • High throughput brightfield scanning for microscopy slides
  • 20X or 40X objective
  • Automatic slide loading, previewing and scanning
  • Utilizes 4MP CMOS camera with 130 fps speed
  • 0,24 um/pixel resolution with the combined 20X/0.8 NA objective (equivalent to 40X  magnification)
  • Free software for viewing (Pannoramic or Case Viewer available from 3DHISTECH)
  • View images from computer screen with different magnifications
  • One file / slide
  • Equal background in all images
  • Choose extended focus or Z-stack for increased layers of focus
Acknowledgement in publications

By using our services, customers agree to acknowledge the Histoscanner Core Facility when publishing their results. Here is one example of a sentence that can be used:

  • "The facilities and expertise of the BI Histoscanner core facility at the University of Helsinki, supported by HiLIFE, are gratefully acknowledged."