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MAN-10152-01 for software v2.5
Select ROIs & Segment
Draw ROIs
Choose from geometric shapes (circle or rectangle), custom polygon , or grid ROIs.
For custom standalone RNA- NGS assays (without Whole Transcriptome Atlas or Cancer
Transcriptome Atlas), ensure that the ROI selection strategy includes a sufficient number of ROIs of
sufficient size, or the resulting NGS library may not contain enough material for accurate library QC. A
general guideline for a standalone custom RNA-NGS assay of 20 targets is a minimum collection area
2
of 425,000 µm
(equal to, for example, 54 circular ROIs of 100 µm diameter), per pooled library. See
GeoMx DSP NGS Readout User Manual
IMPORTANT:
Do not establish ROIs and attempt to collect aspirate from areas of scan with poor
focus, as this can cause instrument damage.
Standard Geometric Shapes
1. Select a shape button (circle or rectangle) from the
Scan Workspace
(see Figure
2. Click in the corner of the area you would like to
designate as an ROI and drag your mouse to the
desired size.
3. Release the mouse click to complete the ROI. This
most- recently applied ROI will now have a number
designation.
4. To adjust, click and drag the center point of the shape to move the shape. Click and drag a
white perimeter point to re-size the shape.
For protein analysis, the diameter of a circular ROI should be greater than 50 µm (200 µm is
recommended). ROIs that will be segmented should be greater than 100 µm (300 µm is
recommended). For RNA analysis, the diameter of a circular ROI should be greater than 200 μm (or
400 μm if segmented). Open the ROIs List (see page 43) to check the dimensions of established ROIs.
Maximum ROI dimensions are 660 µm x 785 µm. A maximum of 380 ROIs can be placed on a single
scan.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
(MAN-10153) for more information.
25).
GeoMx DSP Instrument User Manual
Figure 25: Scan Workspace square
ROI button
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