Scanning

We run a digital slide scanning service (Pannoramic 250 FLASH II, 3DHISTECH) for both bright-field and fluorescent slides using either 20x or 40x air objectives. 

Pannoramic 250 Flash II

  • High throughput bright field and fluorescence scanning for microscopy slides 
  • Capable of scanning 250 sides / run
  • Z-stack and extended focus options
  • Automatic slide loading, previewing, barcode reading and scanning
  • 0,24 um/pixel resolution with the combined 20X/0.8 NA objective and 0,12 um/pixel resolution with 40X/0.95 NA objective
  • Free software for viewing and annotating digitalized slides can be downloaded from manufacturers webpage

Filters (Zeiss), (Semrock)

 

Filter

Ex(nm)

Mirror(nm)

Em(nm)

1.

Transmitted light

 

 

 

2.

DAPI-1160B (Semrock)

387/11

409

447/60

3.

Cy5-4040C (Semrock)

628/40

660

692/40

4.

25HE Dapi/Fitc/TxRed

405+495+575

435+510+600

460+530+625

5.

38HE GFP

470/40

495

525/50

6.

43HE Cy3

550/25

570

605/70

7.

64HE mPlum

587/25

605

647/70

Pricing information

  University of Helsinki groups Biocenter Finland network Universities and HUS Other customers
Bright-field scanning      
20x objective      
focusing to one plane 3 € 3 € + VAT (24 %) 6 € + VAT (24%)
extended focus or Z-stack 5 € 5 € + VAT (24 %) 10 € + VAT (24%)
40x objective      
focusing to one plane 5 € 5 € + VAT (24 %) 10 € + VAT (24%)
extended focus or Z-stack 7 € 7 € + VAT (24 %) 14 € + VAT (24%)
Fluorescent scanning 20€/h
(minimum charge 5€/slide)
20€/h + VAT (24 %)
(minimum charge 5€+ VAT/slide)
40€/h + VAT (24 %)
(minimum charge 10€+ VAT/slide)
Manual processing of slides
(e.g. cleaning and marking)
20€/h 20€/h + VAT (24 %) 40€/h + VAT (24 %)

Manual processing fee is applied when

  • Slides need to be cleaned of dust or stains 
  • Excess mounting media needs to be removed
  • The coverslide needs to be trimmed
  • The contrast is not sufficent for automatic detection of sections

GBU wel­comes slides for test scan­ning free of charge!

How to prepare the slides

Please inform us on the number of slides and desired scanning mode by filling out the order form below and emailing it to us. We will give you an estimate of the schedule and agree on possible test scans. If you want to scan fluorescent slides, we would like to set the exposure times for each channel with you and do a test scan before scanning the whole series. We can also do test scans for bright field slides if you need to decide between 20x and 40x and whether to have the extended focus feature or not. 

For scanning to be successful the slides have to fulfil the following requirements

  • Width 24-26 mm, length 75-76 mm, thickness 0,9-1,2 mm
  • Mounted with hardening mounting medium
  • Coverslide does not protrude over the edge of the slide
  • No excess mounting medium on the slide

For optimal image quality and easy scanning

  • Avoid bubbles under the coverslide.
  • Place sections in the middle of the slide (scannable area is inside the crosses and about 4 mm from the frosted end).
  • For bright field slides, counterstain if necessary to get your sections to stand out.
  • Dust particles, immersion oil stains, and marker stains will impact image quality.

For services in tissue processing, sectioning and staining at the University of Helsinki, please contact one of the core facilities in the Histotechnology and animal pathology platform (HiLAPS).

Delivering the slides

You can bring your slides in person or send them via mail. All projects have to be agreed with GBU staff by email before delivering the slides. Fluorescent slides are stored in +4 ºC. We will let you know when you can collect the slides, or we can send them back by University of Helsinki internal mail. 

Naming the data files

If you are scanning several slides and you want the data files to be named according to your samples, please provide an excel sheet with the sample names. If no name is defined, the scanner will generate one for each slide based on its position in the magazine. The label on the frosted end of the slide will be associated with the scanned image. 

Image files

Image files are provided in MRXS format and can be viewed with 3DHISTECH viewing softwares (Pannoramic Viewer, CaseViewer) which can be freely downloaded from the manufacturers webpage. You can also view your images using Biomedicum Imaging Unit imaging workstations.

Please note that the size of the image files can be very large (up to several GBs/slide). Images are saved on the scanner computer immediately following scanning. The network connections of the scanner computer are restricted and for the brightfield images it is recommended you copy the files straight from the computer to your own portable drive. As the fluorescent images are usually smaller, it is possible also to distribute them using Funet FileSender server.

If you find images of suboptimal quality, please contact GBU for rescanning the slide. For difficult samples it is possible to use more focusing points or apply extended focus option.

Please note that GBU can store the image files from your scanner run only temporarily.

Image analysis

There are several ways to analyze your digitalized slides, including the following:

3DHISTECH image analysis modules
Faculty of Medicine in Helsinki currently holds a license for HistoQuant module, which is a histological segmentation module identifying tissue elements based on the color and intensity of the image pixels. HistoQuant can be used with Biomedicum Imaging Unit imaging workstations.

Systems Biology Unit located in Biomedicum 1 provides consultation for imaging related biological experiments, and the analysis of images produced from such experiments. The SBU services include experimental design, image processing/analysis, data analysis and visualization of the analysis, as well as bioimage informatics infrastructure and method development, deployment and training.

Citation

If you publish images generated by the GBU service, please acknowledge us in your paper in the following way:

"Images were generated using 3DHISTECH Pannoramic 250 FLASH II digital slide scanner at Genome Biology Unit supported by HiLIFE and the Faculty of Medicine, University of Helsinki, and Biocenter Finland.”