Frequently Asked Questions

How do I open scanned slide images?

  • Scanned images generated on the Leica Aperio AT2 can be opened using Leica’s ImageScope software (Windows) or QuPath (iOS).
  • Scanned images generated on the Zeiss Axio Scan.Z1 can be opened using Zeiss ZEN Blue lite (Windows) or or QuPath (iOS).

If you are new to ZEN, please check our Quick Start Guide!

I have a project in mind, can I request a consultation?

Yes- project consultation can be requested through the service request form. Please select ‘Consultation’ in question 1 and continue filling the remainder of the survey.

How are GeoMx Digitial Spatial Profiling ROIs/AOIs selected?

Majority of ROI’s/AOI’s are selected one of 2 ways:

  1. Morphology mask guided. Each slide is stained and scanned for 4 immunofluorescence biomarkers. These markers are used to autogenerate segmented regions based on their expression. For example, Pan-cytokeratin would be used to generate the tumor segmented region.
    • Ready to use morphology kits are available to be purchased by the researcher from Nanostring.
    • Custom masks/antibodies can be optimized by MAPcore on an individual bases for a fee.
  2. User guided. Researchers can request to be on-site during the DSP protocol to select the ROIs themselves.

For more comprehensive explanation of ROI selection please click the link to the DSP manual.

How many ROIs/AOIs can I have per DSP project?

The number of ROIs per project is dependent on the assay being run.

Assayslide/AOI capacity
Protein nCounter readout12 slides and 576 AOIs (whichever comes first, can purchase extra AOI capacity at additional cost)
RNA nCounter readout12 slides capacity
AOI capacity is purchased separately in increments of 96 AOIs
RNA NGS readoutAOI capacity is purchased separately in increments of 96 AOIs

Please see the slide planning guide for further information.

How many biomarkers can be in a multiplex panel?

Multiplex panels come in 2 flavors- brightfield/chromogenic and fluorescence.

  • Brightfield multiplex panels currently have the capacity of 4 biomarkers plus hematoxylin (5 colour). However, depending on panel composition, more biomarkers can be added. Please note that multiplex chromogenic panels must be scored by-eye by a pathologist and cannot be scored using automated software.
  • Fluorescence multiplex panels have capacity for 6 biomarkers plus DAPI (7 colour). Please note that MAPcore is current optimizing our scanning protocols and are expecting to expand our multiplex IF capacities to 8 biomarkers plus DAPI (9 colour). These panels can be scored using automated software by MAPcore (additional charges apply) or by researchers using digital pathology software of their choice (ex. QuPath or Halo).

What materials do I need to provide for a service request?

For each provided service, MAPcore will typically provide majority of reagents. However, researchers will need to to provide the below material for each service requested:

ServiceClient provided
Coring– tissue blocks
– regions of interest circled (by pathologist or researcher)
Scrolling– tissue blocks
Macrodissection– tissue blocks
Sectioning– tissue blocks
TMA construction– tissue blocks
– regions of interest circled (by pathologist or researcher)
Laser Capture Microdissection– tissue blocks
Hematoxylin and Eosin staining– tissue (please either request microtomy for provided blocks or provide pre-cut, unbaked slides)
Single Biomarker IHC– tissue (please either request microtomy for provided blocks or provide pre-cut, unbaked slides)
– antibody (if not listed in our MAPcore catalog)

If optimizing an antibody not listed in our catalog, please provide control tissue.
Chromogenic Multiplex IHC– tissue (please either request microtomy for provided blocks or provide pre-cut, unbaked slides)
– antibody (if not listed in our MAPcore catalog)

If optimizing an antibody not listed in our catalog, please provide control tissue.
in-situ Hybridization (RNAscope)– probes can be purchased by the researcher from ACD Bio
– control and final tissue (please either request microtomy for provided blocks or provide pre-cut, unbaked slides)
nanoString GeoMx® Digital Spatial Profiler– tissue blocks provided at least 2 weeks before the experiment is to be run
– GeoMx Core and Module probes
– GeoMx Morphology kits
– Hyb code reagent packs
Brightfield Whole Slide Scanning– *Pre-cleaned coverslipped glass slides

*unless another service is requested to generate slides
Fluorescent Whole Slide Scanning– *Pre-cleaned coverslipped glass slides

*unless another service is requested to generate slides
Research Pathologist Assessment – *Digital slide scans

*unless another service is requested to generate slides

Can I use an existing nCounter panel for DSP?

No. The GeoMx nCounter assays have been developed with unique UV-cleavable probe sets. However, 10 custom probes can be added to any nCounter GeoMx DSP panel. If you are interested in adding custom probes please contact us for more information.

Please explore the currently avaiible probes lists from NanoString for the GeoMx DSP:

*NGS assays are not yet available through MAPcore but is expected in the near future. Please monitor this site for updates.