Categorrizing Signals: Nucleus, Spot signals

Task: seperate three types of localization automatically:
--> same type of task appears in many applications.

A: small spots a bit remote from the nucleus
B: Large aggregate of replication sites, surrounding the nucleus.
C: diffuse cytoplasmic signal

In general, thresholding strategy will be the key for this type of problem .

Strategy:

1. Threshold DAPI at a sufficient level. (segment each cell according to nucleus)
--> do nucleus signals are always with similar intensity?
-- if not, threshold level must be set for each nucleus.
-- according to the size of nucleus?
-- dynamic thresholding --> determine the best threshold level.

2.a. Dialate Thresholded DAPI signal, to make a mask for each cell.
--> define iteration of dialate operation.
2.b. Get the centroid of the Dapi signal.
--> particle analysis

3. within the mask (=ROI), threshold to select high intensity signal.
4. count particles within the mask, get average area and intensity.

5. plotting parameters
- distance from the nucleus
- average area
- average intensity
- number of counts in graphs. (3D graph?)

--> can populations be seperated? (cluster analysis)