Biology Reference
In-Depth Information
3. Press “OK” to compute the heat map.
4. You should see a color bar on the top left of the visualization
area, and the cells are now colored by area.
To compute the expression intensity of an intracellular marker
(e.g., nuclear or cytoplasmic marker), the data must have been
acquired at the same time as the cell wall marker in a different
channel so that there is no displacement between the two.
3.7 Computing
Marker Expression
Intensity
1. Load the stack containing the marker of interest and the seg-
mented mesh in the same stack.
2. Use the mesh process “Project Signal” in the “Signal” folder.
The distances should be set so as to select most of the cells (
see
Note 14
, Fig.
4f
).
3. Use the mesh process “Heat Map” in the “Heat Map” folder.
The heat map type should be set to “Area” and the heat map
visualization should be set to “Total Signal” (
see
Note 15
,
Fig.
4g
). You can also save the result to a spreadsheet fi le for
further analysis.
Both area and fl uorescence expression analysis can be compared
over different time points:
1. Load both segmented meshes with the appropriate signal pro-
jection, making sure they are both visible.
2. Select the stack tab for the time point that you want to use to
visualize the result.
3. Use the mesh process “Heat Map” in the “Heat Map” folder.
4. Select the parameters for the analysis desired (i.e., area,
signal).
5. Tick the “Change map” check box and set the other parame-
ters for the change map. If you are analyzing two time points
of growth, and are visualizing the result on the fi rst time point,
then you would set the change map to “Increasing.” This will
color the cells with the most expansion in red and those with
the smallest in blue. MorphoGraphX will auto-scale the color
range to the data. This behavior can be overridden by using
the “Use manual range” option and is important when com-
paring different repeats of an experiment.
3.8 Comparing Data
from Two Time Points
4
Notes
1. Most microscopes offer a false coloring of the image using
contrasted colors for both ends of the spectrum. Use this mode
and ensure you have a few black and a few saturated pixels in
the zone of interest. For the purpose of cell segmentation, you
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