fill holes after segReduce

matlab/+Segment/frameSegment.m

@@ -89,6 +89,9 @@ end
 % allocateShake (below) assigns each discarded pixel to it's closest
 % touching segmentation using a morphological region fill
 bw=Segment.aiAreaOpen(bw,min_radius_pixels);
+if ~segParams.isPhase
+    bw=bw|imfill(bw,'holes');
+end
 bw2=bw;
 bPhaseReduce=segParams.isPhase || segParams.bCytoplasmic;
 % if prod(size(im))>1e9
@@ -96,18 +99,12 @@ bPhaseReduce=segParams.isPhase || segParams.bCytoplasmic;
 %     bPhaseReduce=true;
 % end
 bw=Segment.segReduce(bw,bwLog,bPhaseReduce,min_area_pixels,min_radius_pixels);
-
 if ~segParams.isPhase
     bw=bw|imfill(bw,'holes');
 end
 
-% if prod(size(im))<1e9
 [L,num,bwBoundary]=Segment.allocateShake(bw,bw2,min_radius_pixels,segParams);
 [L2]=bwlabeln(bw2); % used to mark original cc for segCC field
-% else
-%     [L,num]=bwlabeln(bw);
-%     L2=L;
-% end
 
 if bEnsemble
     if size(bw,3)>1
@@ -129,6 +126,9 @@ end
 CC=bwconncomp(L);
 for n=1:num
     idx=CC.PixelIdxList{n};  
+    if length(idx)<3
+        continue
+    end
     if is3D(im)
         newCell=Segment.frameSegment_create_3D(idx,size(bw),chan,t);
     else