SN | Filter |
Excitation (nm) |
Mirror (NM) |
Emission (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 |
Starting from 1.9.2022, new pricing applies. Extended focus and fluorescent scans are invoiced in a time-based manner.
In addition to per-slide or hourly charges, a project fee is introduced for each batch of slides delivered to FinGEEC and invoiced to a single customer. This fee covers slide inspection, scanner loading, and profile creation for each scan.
ITEM |
Fee (€) UniveRSITy of Helsinki |
fee (€) Biocenter Finland Affiliates |
fee (€) other customers (+vat) |
---|---|---|---|
Project fee | 25 | 25 | 55 |
Bright-field scan | |||
20x bulk | 1,00 | 1,00 | 1,15 |
40x bulk | 2,00 | 2,00 | 2,30 |
20x Standard | 2,50 | 2,50 | 3,90 |
40x Standard | 5,00 | 5,00 | 7,30 |
BF extended focus or Z-stack (per hour) | 12,00 | 12,00 | 15,50 |
Fluorescent scanning (per hour) | 12 | 12,00 | 15,50 |
Due to the large variation of scan time in extended focus and fluorescent scanning, all these slides are invoiced based on scanning time.
You can ask for a rough estimate of cost, but we don't give binding quotes.
A test scan of one representative slide can be made for free to estimate the cost.
See below some tips to reduce scan time.
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).
Fluorescence scanning of one slide may take anything from a few minutes to more than 8 hours. Billing for fluorescent scans is time-based. Scanning time depends on the size of the scanning area, objective used (20x/40x), number of layers (extended focus/one plane), number of channels, and exposure times on each channel. Please, consider the following to make scanning as fast as possible while still getting the quality you need:
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 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 FinGEEC for rescanning the slide. For difficult samples, it is possible to use more focusing points or apply extended focus option.
Please note that FinGEEC can store the image files from your scanner run only temporarily.
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.
If you publish images generated by Finnish Genome Editing Center (FinGEEC), please acknowledge us in your paper in the following way:
Images scanned after 19th April 2023:
"Images were generated using 3DHISTECH Pannoramic 250 FLASH III digital slide scanner at Finnish Genome Editing Center supported by HiLIFE and the Faculty of Medicine, University of Helsinki, and Biocenter Finland.”
Images scanned before April 19th, 2023:
"Images were generated using 3DHISTECH Pannoramic 250 FLASH II digital slide scanner at Finnish Genome Editing Center supported by HiLIFE and the Faculty of Medicine, University of Helsinki, and Biocenter Finland.”