nanoString GeoMx DSP User Manual page 113

MAN-10152-01 for software v2.5
Troubleshooting
Issue Possible cause
Accidentally ran User error
experiment with
wrong set of
probe kit
configuration
(.pkc) files
selected
I can't get Overcomplicated
ROI segments segmentation
to look the way I strategy
want them
After approving Root cause can
ROI, instrument only be determined
does not from log files, but it
proceed to is often due to
collect tissue extending
into tip calibration
area of slide, or
low volume of
Buffer H or S.
Plate status Temporary
indicator shows hardware or
a red well during software error
collection caused a skipped
segment or ROI
For nCounter User error
Readout:
Collected into
the wrong row,
or I don't have
HybCode to
match the
collection row.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
GeoMx DSP Instrument User Manual
Suggested action
See instructions on amending .pkc after the experiment
page 69.
A complex segmentation strategy may lead to ROI segments
that don't meet your expectations by eye. In other words, you
can't get the segments to capture the cell regions you wish to
capture. In this case, it's recommended to try a very basic
segmentation strategy - for instance, each segment with one
definition (e.g. +PanCK). A simple strategy may produce
segments that better capture the cells of interest.
Contact GeoMxSupport@nanostring.com
situation. This issue can often be prevented by examining slides
to ensure that tissue does not exceed Scan Area boundary
Figure 101); wiping the bottom of each slide clean with 70%
ethanol and a Kimwipe before the instrument run, and ensuring
Buffer H and S have 20% volume or more prior to starting a run.
Typically, the hardware or software recover and proceed with
collection. For assistance, contact
GeoMxSupport@nanostring.com.
The collection row must match the Hyb Code letter (A, B, C,
etc). You may re-scan the slide(s), selecting different ROI, and
collect into plate rows that match the Hyb Code you have on
hand, or order additional Hyb Code to match the row of the
collected aspirates. Contact
for further guidance.
to evaluate the
GeoMxSupport@nanostring.com
on
(see
113