NEIDL Comparative Pathology Laboratory (NCPL)

Multispectral Whole Slide imaging (mWSI)

Currently located at the National Emerging Infectious Diseases Laboratories (NEIDL), the Vectra Polaris is managed by NEIDL Comparative Pathology Laboratory (NCPL) staff. It will be moved to the Integrated Biomedical Imaging Services (IBIS) space in the Housman (R) building, 8th floor, 72 East Concord St., Boston, when renovations are complete. The renovations will include development of a dedicated image analysis suite with four perpetual licenses of inFORM image analysis software that will afford multispectral unmixing of whole slide images and quantitative analysis such as positive pixel analysis, cell phenotyping, and spatial analysis.

Instruments

Akoya Biosciences Vectra Polaris Whole Slide Imaging System

 

 

 

 

 

 

 

 

Overall Benefit

The addition of a Vectra Polaris Quantitative Pathology Imaging System to the BUSM research community includes:

  1. Enhanced utilization of biological specimens derived from research projects by affording the capacity of high throughput whole slide image acquisition of both brightfield and high-plex fluorescent images-up to six colors plus DAPI using the rapid acquisition MoTIF workflow.
  2. Increased analytical sensitivity/enhanced signal to noise ratios through multispectral unmixing of acquired images including removal of autofluorescence signals.
  3. Enhanced precision and objective analysis through quantitative characterization of morphomolecular signatures with spatial context afforded through an integrated image acquisition and advanced image analysis pipeline.
  4. Generation of continuous pathomics datasets affording correlations with other relevant biological datasets (i.e., clinicopathologic, transcriptomics, etc.) enabling for more rigorous and integrated research approaches to further elucidate clinicopathologic correlates of disease.

Akoya Biosciences Vectra Polaris Specifications

Slide Capacity 80+ (continuous loading)
Output File Format .qptiff and .im3
Objectives 5, 10, 20, 40x
Image Acquisition Brightfield and 9-channel fluorescence-30 minutes to an hour
InFORM Image Analysis Features Tissue segmentation (machine learning), cell segmentation, phenotyping (machine learning), scoring, spatial analysis
Scan Method Tile
Z-Stacking No
Liquid Crystal Tunable Filter Yes
Continuous Workflow Yes
Multispectral Imaging with Unmixing Yes
Integrated Spectral Unmixing Yes
Autofluorescence Removal Yes: Quantitation and isolation using automatically selected AF filter
Synthetic Spectra for Unmixing Yes
Multiband Epi-Fluorescence Filters Yes
Flash LEDs for Photobleaching Protection  Yes
Local Support Team Sales Specialist/Application Scientists (PhD)/Service Engineer (PhD)/Bioinformatics Scientist (PhD)

Vectra Polaris Epi-fluorescence Filter Cube Characteristics

 Slot Cube Band Excitation (nm) Emission (nm)
Cut on Cut off Cut on Cut off
1 DAPI/NIR DAPI 383 391 411 697
NIR-near infrared 719 751 769 847
2 FITC FITC 460 500 511 720
3 Cy3 Cy3 530 560 574 720
4 Texas Red Texas Red 567 589 604 710
5 Violet/Cy5 Opal 480 405 443 458 578
Cy5 593 647 665 734
6 MBA DAPI 377 405 440 466
Opal 570 528 549 563 579
Opal 690 626 672 691 727
7 MBB Opal 480 405 443 46 496
Opal 620 580 601 615 651
Opal 780 717 753 767 898
8 NBC Opal 520 474 499 523 541
9 Sample AF Sample AF

Recommended Fluorescent Dyes

Akoya Opal Dyes Alexa/ATTO Dyes Biotium CF® Dyes Cyanine Dyes Other
Spectral DAPI
Opal 480 AF405
Opal 520 AF488 CF488A Cy2 FITC
Opal 540 AF514
Opal 570 AF555 CF543 Cy3 TRITC
Opal 620 AF594 CF594 Cy3,5 Texas Red
Opal 650 AF635 CF640R Cy5
Opal 690 AF660/680 CF680R Cy5,5
Opal 780 AF750 Cy7
Highlighted dyes are part of the MOTiF rapid 7-color acquisition protocol and recommended for maximum efficiency and quality of whole-slide imaging.

Services provided by staff include:

  • Core competency training on the operation of the Vectra Polaris image acquisition.
  • Assisted or independent use of the Vectra Polaris whole slide scanner, with the latter only available to those approved by NCPL staff.
  • Guidance in generating multispectral libraries to remove auto-fluorescence and maximize signal to noise ratios of images using inForm.
  • Assistance and training in the generation of quantitative pathology outputs using inForm.
Services
BU Internal Rates External Rates
Brightfield Unassisted/Slide $12 $21
Brightfield Assisted/Slide $15 $27
Fluorescence Unassisted/Slide $20 $36
Fluorescence Assisted/Slide $25 $44

How to Schedule

Please login to iLab system to schedule equipment time or services. For new users please follow the steps outlined in Information for New Users.

Usage and Training

Training is mandatory for all new users and requires:

  • Scheduling of two consecutive 1-hour sessions of “Assisted Use” for practical in-person training.
  • Users are expected to bring their own slides for scanning during the training session.
  • A combination of both brightfield and fluorescent slides is recommended to familiarize users with developing scan profiles for each of these formats.

Please contact us to schedule training or assisted use. Once users have been trained, time on the instruments may be scheduled.

Training Videos

New users should watch these short videos prior to attending in-person training held by core staff:

  1. How to power cycle the instrument.
  2. How to load slides into carries.
  3. How to load carriers into the instrument.
  4. Polaris software overview which shows you how to scan slides, take references and acquire spectra from library slides.
  5. inForm analysis covers the basic of image analysis using inForm.

We require that all users cancel sessions 24 hours before the scheduled start time. Failure to cancel will result in the user (or PI) being billed for the entire scheduled duration.

Acknowledgments

The Vectra Polaris was funded by the NIH Award Number S10OD030269. We greatly appreciate acknowledgement of NIH S10OD030269 in publications when authors use our equipment and/or assistance in their research.

Contact

Nicholas Crossland, DVM, DACVP
NCPL Director
(617) 358-9285 | ncrossla@bu.edu

Hans Gertje, BS, HTL(ASCP)CMQIHCCM
NCPL Lab Supervisor
(617) 358-9139 | hgertje@bu.edu

Location

Boston University School of Medicine
National Emerging Infectious Diseases Laboratories (NEIDL)
620 Albany St., Boston, MA 02118

View BUMAPS

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