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University of Helsinki Biocentrum Helsinki Genome Biology Unit
 

Genome Biology Unit (GBU)

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Contact information:

tel: 02-941 25581
bch-gbu@helsinki.fi

Kaisa Laajanen M Sc
Susanna Räsänen B Sc (pharm)
Tea Vallenius MD, PhD

 

 

 

 

 

 

3D HISTECH scanning

Non-profit GBU slide scanning service is running in Biomedicum Helsinki 1 (B319a). We have the 3DHistech Pannoramic 250 FLASH II digital slide scanner capable of both light and fluorescent imaging using either 20x or 40x objectives.

Come and see with your own slide (free test slide)!



1. 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

  • For more information click here

Fluorescence filters available:
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

 

 

 

 

 

 

 

 

 

 

RESERVATIONS

Please contact GBU personnel for making the reservations (bch-gbu@helsinki.fi), also indicating the number of slides you wish to have digitalised.

PREPPING THE SLIDES

Only slides closed with compounds that harden into permanent mount e.g. depex are accepted for scanning. Please pay attention to the quality of your slides, preferably having the sections in the middle and not too much excess mounting medium on the edges. Remember that the coverslip must not protrude at all over the edges of the slide!
Please see the instructions for prepping slides.

For services in tissue processing, sectioning and staining in Biomedicum 1 Helsinki, please contact Tissue Preparation and Histochemistry Unit.

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 (we will inform later on the possibility of printing barcode labels to the slides). If no name is defined, the scanner will generate one for each slide based on its position in the magazine.

PRICING

The slide scanning service provided by Genome Biology Unit is priced as follows (until further notice):

3DHISTECH slide scanning (University of Helsinki), €/slide, VAT 0%

20x bright field scanning, automated run,
- 3€/slide routine scanning focusing to one plane
- 5€/slide with extended focus or Z stack

40x bright field scanning, automated run,
- 5€/slide routine scanning focusing to one plane
- 7€/slide with extended focus or Z stack

Fluorescent scanning
- 20€/h, minimum charge 5€/slide

If the routine scanning is not sufficient for your slides:
- Manual scanning (automated sample detection not possible) 20€/h
- Cleaning and scraping of slides prior to scanning 20€/h

GBU welcomes slides for test scanning free of charge!

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 manufacturers webpage (currently only available for windows). 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 R: drive 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.

 

ImageJ

Webmicroscope

JPEG2000 Virtual Slide microscope

If you know other suitable image analysis tools for analyzing digitalized slides, please inform us!