Scanning

IMPORTANT INFORMATION! Starting from January 7th 2025, the Pannoramic 250 Flash III slide scanner will no longer be operated by GBU. GoEditStem platform core unit FinGEEC will manage the scanner service after this date. All future scanning orders should be done by emailing the filled order form to fingeec-support@helsinki.fi. 

Since April 19th 2023 the scanner is upgraded from Pannoramic 250 Flash II to Pannoramic 250 Flash III
Pannoramic 250 Flash III

• 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)

Pricing information

New prices are applied starting 1.9.2022. 
All extended focus scans, as well as fluorescent scans, are now invoiced in a time-based manner.

In addition to price per slide or per hour there is now a project fee, which is applied to a batch of slides delivered to GBU at one time and invoiced to a single customer. The project fee covers inspecting and loading the slides in the scanner, and making profiles for the scan. 

Bulk scan 

• Minimum billing for ten slides. 
• Single plane only, 20x or 40x, bright field
• Requires clear staining that can be automatically detected by the scanner (e.g. HE on good-quality sections of dense tissues, low background and no fatty tissue)
• Only clean slides with well-aligned coverslide (dirty, broken or skewed slides will be omitted from the scan or invoiced as standard slides)
• No quality control for individual slides, re-scans can be requested and will be charged with the standard price.
• Limited filesize (very large sections in 40x may be too much)
• File storage only 1 month
• GBU technicians will evaluate the suitability of each batch for bulk scan

Standard scan

• Any number of slides
• Single plane, 20x or 40x, bright field
• Each image is checked and re-scans are included in the price
• File storage 6 months
• Slides still have to be clean

Extended focus and fluorescent scans

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.

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 (standard slides)
• 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).

Make fluorescent scanning faster and more cost efficient

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 don’t need all the sections on the slide or if you only need a partial section to be scanned, you can mark the areas to be scanned yourself. Draw the marker very close to the section edge (<1 mm is sufficient). Use a thin black marker.
• Magnification: 40x takes at least four times as long as 20x.
• Extended focus or Z-stack take longer than single-plane scans. Extended focus is done from 7 layers as a default. The number of layers can be decreased.
• Exposure times should be set as low as possible for each channel.

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 of FinGEEC service, please acknowledge us in your paper in the following way:

Images scanned after April 19th, 2023:
"Images were generated using 3DHISTECH Pannoramic 250 FLASH III digital slide scanner at Genome Biology Unit OR 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 Genome Biology Unit OR Finnish Genome Editing Center supported by HiLIFE and the Faculty of Medicine, University of Helsinki, and Biocenter Finland.”