Slide scanning and other services

Other services:

For these services, please contact the core personnel.

  • iPS cells
  • Isolation of ES cells
  • Ovary transfer
  • Importing of mouse lines
  • Shipping of mouse lines
  • Microscope slide scanning service
  • Visiopharm image analysis software

Microscope slide scanning service and image analysis software

The scanner is located at TTP core facilities in lab 478B, 4th floor in Kieppi building.

For further information, please contact TTP core personnel:
reetta.vuolteenaho(at), salla.kangas(at), anne.heikkinen(at)

Slide scanner information [PDF]

Hamamatsu NanoZoomer S60 slide scanner

  • NanoZoomer S60 slide scanner is for scanning histological specimen
  • Scanner capacity at one run is 60 slides (or 20 double sized slides)
  • 20x and 40x modes
  • Price: 75 cents/slide
  • At the moment, the images will be delivered by using FileSender, or they can be stored to external hard drive/memory stick

Sample quality

  • Mount with permanent mounting media and let dry at least 24 hours
  • Coverslip must not protrude over the edge of the slide at all
  • Slides should be cleaned of excess mounting media
  • No text or other markings in the scanning area (interferes with autofocus)
  • No broken slides or coverslips -> they can damage the scanner!
  • Please, include an excel file with the names of the slides (in the same order in which you have given them)

Viewing and exporting the images

  • You can view your scanned slides and export images using free software NDP.view2, freely available at Hamamatsu homepage and in Software Center for UNIV-computers.

Visiopharm image analysis software

  • Visiopharm software is used for image analysis-based quantification of tissue properties
  • Analysis Protocol Packages (APPs) are small programs to automatically analyze brightfield and fluorescent images
  • APPs are either self-made or they can be purchased from Visiopharm APP center
  • Usage of Visiopharm image analysis software is reserved through iLab system and it is free of charge

Visiopharm APP design service

  • TTP core provides service for APP design to answer specific research questions of customers
  • Before starting, please contact us for the kick-off meeting to plan the image analysis project
  • The service fee is based on the amount of work required for designing the APP 
  • In case of publication, the contribution of TTP shall be acknowledged 
  • We provide user training for Visiopharm software and help for troubleshooting

Last updated: 16.12.2020