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

For further information, please contact TTP core personnel:


Slide scanner information [PDF]

Hamamatsu NanoZoomer S60 slide scanner

  • NanoZoomer S60 slide scanner is for scanning histological specimen
  • Accepted slide size is 26 mm x 76 mm or double sized 52 x 76 mm
  • Scanner capacity at one run is 60 slides (or 30 double sized slides)
  • 20x and 40x modes
  • Price: 75 cents/slide

Sample quality and instructions for preparing samples for scanning

Scanning service is requested through iLab.

Slide scanner is located in the lab 478B on the fourth floor in Biocenter Oulu premises. You can bring your slides and external data storage for the images on a shelf into the cabinet on the corridor outside the lab.

  • Scanning service is requested through iLab.
  • Mount with permanent mounting medium and let dry for at least 24 hours
  • Coverslip must not protrude over the slide edge at all
  • Slides should be cleaned off 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!
  • Mark slides with running numbers to keep them in correct order
  • Please, compose an Excel file with the slide/file names (max 20 characters, no special characters or å’s, ä’s or ö’s) in the same order in which you have given them. The sample list Excel file is added in iLab when doing service request for scanning.
  • If you have more than one tissue section per slide, please let us know in the Excel file, if you want only a certain section to be scanned (this can reduce the file size substantially)
  • Put your name/Name of the requester on the box containing the samples, so we will know to whom the samples belong
  • Together with the samples you can bring an external disc for storing the images, or they can be sent to you by FileSender
  • Scanner image format is *.ndpi and you can use the software NDP.view2 to view the images. Software is available in the Software Center

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: 28.4.2021