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MAN-10152-01 for software v2.5
Select ROIs & Segment
Using an External Program for Segmenting
Export images to an external program (such as
ImageJ) to create segments within an ROI.
1. From the ROIs List
(see Figure
the Export All button to export all ROIs for
custom segmenting. Alternatively, export
one individual ROI using the Export button
below the ROI.
2. The system will export files in multi-channel
TIFF format. Save to a desired location.
3. Use the external program to create masks
within the exported ROI. See the GeoMx
DSP: Creating Geometric Segmentation
Masks using ImageJ Guidelines at
https://university.nanostring.com.
NOTE: Segments cannot overlap.
4. Save the segment mask image to your computer as a PNG or single layer TIFF file of the same
resolution and dimensions as the original exported TIFF. Any pixel values greater than zero in
your saved image will be treated as segment area. Zero-value pixels will be treated as empty
space. Return to the Scan Workspace.
IMPORTANT:
the segment name. If the filename has underscores, the system expects the filename in the
following format:
{roi-name}_{segment-name}_{collection-order}_{color}_{tag1}_{tag2}_{tag3}...
All properties after {segment-name} are optional. {color} must be an HTML-style hexcode (like
'10ffcc'). Imported segment names will be truncated at 100 characters, potentially resulting in
non-unique names.
5. Select the Import All button from the ROIs List to import all custom segmented ROIs.
Alternatively, select the Import button below each ROI of interest to individually import the
applicable custom segment mask.
6. Browse to the location of your saved image and select Open. The segments will appear
on the selected ROI.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
37), select
If the filename does not have underscores, then the filename will be used as
GeoMx DSP Instrument User Manual
Figure 37: Scan Workspace ROIs List with Export Image link
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