Core Biotechnology Services

Akoya Vectra Polaris slide scanner





  • Phenochart free slide viewer for the Vectra Polaris can be installed on your own computer via the University's Software Centre or the latest version can be downloaded from the Akoya Bioscience website.

The AIF has purchased a PerkinElmer (now Akoya Biosciences) Vectra Polaris slide scanner with funding from the University Research Equipment and Infrastructure Fund, LD3 and AIF. The system has been installed in RKCSB room 533 but all users will have access to the system.

The Vectra Polaris can be used for bright field slide scanning, multi-colour fluorescence slide scanning and multi-spectral slide scanning.

Using multi-spectral imaging the system can separate up to 9 different colours as well as separating autofluorescence background from the real signal. The system can also be used with filter cubes to separate up to 5 different colours.

The system is optimized for Akoya Biosciences Opal assay kits but other fluorescent markers can be used as well.

For automatic identification of specific tissue types we have now 5 licenses for the integrated inForm image analysis software. One license is installed on the system, one license is with the LCRC, one is installed in the Henry Wellcome Building image analysis room (SURF) and two in MSB 340 image analysis room (inForm and Max).


Pricing system (this is independent from the normal AIF charges, so will be charged extra!!):

  • £16.00 per hour (internal use; subject to change).
  • Large projects please contact Kees Straatman.

External users welcome. Please contact Kees Straatman for availability and pricing.


Available magnifications

There are two objectives on the system

  • 10x/NA = 0.45
  • 20x/NA = 0.75

The physical camera pixel size is 3.5 um.

For fluorescence slide scanning the system gives the options:

 Objective Vectra Polaris options   Binning  Pixel size (µm) Best resolution at 550 nm (µm)
 10x  10x  2x2  1  1.5
 10x  20x  1x1  0.5  0.75
 20x  20x (40x binned)  2x2  0.5  0.9
 20x  40x  1x1  0.25  0.45

The 10x objective scan time will be ~4 times faster than using the 20x objective. Binning results in more signal collected per pixel due to larger pixel size, and a smaller file size.

For brightfield slide scanning only the 20x objective is used. The different pixels sizes are just achieved through binning.

So, actual scan time is practically identical for all resolutions in BF imaging and the advantage of choosing a lower resolution than 40x is that you get smaller file sizes.

Filter cube reference list

  • Opal 480 similar to coumarin
  • Opal 520 similar to Alexa488, FITC, Cy2, GFP
  • Opal 570 similar to Alexa555, Cy3
  • Opal 620 similar to Alexa594, Texas Red-X, RFP
  • Opal 690 similar to Alexa660-700, Cy5.5
  • Opal 780 similar to Alexa750, Cy7

Sample preparation

Use a rectangular coverslip of number 1.5.

Don't use mounting media containing DAPI but use a DAPI staining step before you mount your samples.

Don't use nail varnish to seal your coverslip. The Vectra Polaris has to auto-detect your sample and will use the coverslip edges to detect the area for scanning. Nail varnish might cause the system to fail to detect the coverslip edge. As a result you need to use a hard-setting (curing) mountant and Akoya Biosciences advices to use ProLong Diamond from Invitorgen/ThermoFisher (no commercial interest from AIF) for the Opal dyes, but other curing mountants will probably work as well as long as they can be combined with your fluorescent markers.

If you have to mark the tissue area for sample detection use a blue marker pen for fluorescence samples and a black marker pen for brightfield samples.

Synthetic database

See an overview of the dyes included in the synthetic database:

 Fluors  Fluors
Alexa 488  Cy3 
Alexa 514  Cy3.5 
Alexa 532 Cy5 
Alexa 546  Cy5 
Alexa 555  Cy7 
Alexa 568  DAPI 
Alexa 594 DRAQ5 
Alexa 610  eGFP 
Alexa 633  FITC 
Alexa 647  HCS Blue 
Alexa 660 HCS Deep Red 
Alexa 680 Hoechst 33258 
ATTO 390 Opal 480 
ATTO 425 Opal 520 
ATTO 488  Opal 540 
ATTO 532  Opal 570 
ATTO 550 Opal 620 
ATTO 647N Opal 650 
 ATTO 680  Opal 670 
ATTO Rho12  Opal 690 
ATTO Rho14 Opal 780 
Coumain TexasRed 

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