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GeoMx DSP Instrument User Manual
Select ROIs & Segment
Segment ROIs (optional)
You can designate particular biological targets or combinations of biological targets as sub-
regions, or segments, within your ROIs. To auto- segment all ROIs in the scan, use the
Segments Panel within the Scan Workspace. Alternatively, you can export an ROI image for
processing in an external program, such as ImageJ. See GeoMx DSP: Creating Geometric
Segmentation Masks using ImageJ guidelines in the NanoString University Document Library
at https://university.nanostring.com.
IMPORTANT:
RNAscope can be used to help set the location of ROIs (i.e., place ROIs where a
particular RNA is enriched). The signals from RNAscope, however, are not compatible with the
segmentation algorithm on the GeoMx because RNAscope's signals are punctate. An advanced
approach to leveraging RNAscope with segmentation could be designed by leveraging the Image
Overlay feature (see
Practice Exercise to Establish Thresholds for Segmenting ROIs
1. Select +Add Segment Definition one time
to establish a single definition rule. One gray
Segment Definition box will appear
Figure
30).
Do not use segment names greater than 175 characters.
2. Channel designations determine whether each fluorescence channel (FITC, Cy3, Texas Red,
Cy5) should be included (+), excluded (-), or ignored (∅) as part of the segment rule's
definition. Choose one fluorescence channel and set it to +. Leave the others set to ∅.
3. Show Advanced Parameters and set Particle size to 50 and all others to 0.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
44
Select ROIs on page
36).
(see
MAN-10152-01 for software v2.5
Figure 30: Scan Workspace Segmentation menu
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