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Post Type Selectors
CleanGets rid of small objects. Can choose matrix and radius threshold (used 10 here). Built into Threshold, but not Simple Threshold.
A yellow square with black background Description automatically generatedA yellow and black square with black background Description automatically generated with medium confidence
ComplementInverts a binary.
A yellow square with black background Description automatically generatedA yellow and purple cloud Description automatically generated
SmoothSmooths binary layer by using a sphere of the specified radius. Built into Threshold but not Simple Threshold. Used radius ~ 1 micron here.
A yellow square with black background Description automatically generatedA yellow and black square Description automatically generated
Separate ObjectsSeparates nearby binary objects. Can select number of iterations (chose 5 here). Used color by ID on the binary layer to better show separation. Built into Threshold but not Simple Threshold.
A colorfully colored cube Description automatically generated with low confidenceA colorfully painted box Description automatically generated with medium confidence
Fill HolesCloses small holes in a binary layer. Built into Threshold but not Simple Threshold. Did not have much effect on the example image.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
OpenUses Erode followed by Dilate for a specified number of iterations, which cleans up small noise while leaving bigger objects alone. Used 5 iterations here, which was enough to eliminate most of the small objects.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
ClosePerforms Dilate then Erode for a specified number of iterations, which closes holes in objects. Used 5 iterations here.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
ErodeCompares voxels to their surroundings and sets {1} voxels to {0} if there is a neighboring {0}, which shrinks objects. Can choose matrix and number of iterations, used 2 here.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
DilateCompares voxels to their surroundings and sets {0} voxels to {1} if there is a neighboring {1}, which expands objects. Can choose matrix and number of iterations, only used 1 here and the binary region was still significantly expanded.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
Close HolesAnother option to fill small holes in a 3D layer. Can choose matrix and number of iterations, unlike Fill Holes. However, using 10 iterations did not have much effect.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
Circular Open/Circular Close/Circular Erode/Circular Dilate/Circular Clean/Circular Close HolesAlternate methods of performing the operations above, using a sphere of the specified radius instead of a square matrix of voxels.
Linear Open Z/Linear Close Z/Linear Erode Z/Linear Dilate ZMore options for matrix-based image processing but use linear matrices in the Z-direction. Can choose number of iterations, the example here is 3 iterations of linear dilate, which has the effect of extruding objects in the Z direction. These options basically make objects more cylindrical and less conical.
Yellow spots on a black background Description automatically generatedA yellow and black background Description automatically generated
CentersMarks the geometric center of each binary object.
A map of different colors Description automatically generatedA purple and green lights Description automatically generated with medium confidence
CentroidsMarks the center of mass of each object, requires a color layer in addition to the binary to calculate density. Brighter parts of the image are weighted more.
A map of different colors Description automatically generatedA purple and green lights Description automatically generated with medium confidence
Distance FunctionCreates a new floating point layer that stores each {1} voxel’s distance to the nearest {0} voxel.
A yellow square with black spots Description automatically generatedA red and black square Description automatically generated
Convex HullExtends object boundaries until objects become convex. Clearly encountered a bug in the example.
A colorful puzzle pieces Description automatically generated with medium confidenceA red rectangular object with black border Description automatically generated
Medial AxisMarks each object’s medial axis, which somewhat resembles skeletonizing.
A colorful background with black and pink spots Description automatically generated with medium confidenceA colorful lines on a black background Description automatically generated
WatershedFloods regions from either bright areas to dark areas or dark areas to bright areas. This makes all of the space filled except for borders between objects. If binary is inverted, the boundary is left.
A colorful background with black background Description automatically generated with medium confidenceA colorful background with many different colors Description automatically generated
Grow ObjectsExpands objects by the specified radius but keeps them as separate objects from each other.
Grow RegionsExpands objects until their borders have intensity of the specified bounds. Can choose bright regions or dark regions.
SkeletonSkeletonizes 3D objects, which drastically reduces volume while keeping general extent of objects.
A colorful squares on a black background Description automatically generatedA blurry image of colorful lights Description automatically generated
Detect BranchingTakes a skeletonized layer and puts voxels at branch points.
A colorful lines on a black background Description automatically generatedA purple and green background Description automatically generated with medium confidence
Detect EndingsPuts voxels at ending points of a skeletonized layer.
A colorful lines on a black background Description automatically generatedA purple and black sky with many small colored dots Description automatically generated with medium confidence
Filter ObjectsPreserves objects meeting the selected criteria while removing all others. Takes a binary and a color layer. Lots of options to choose from, such as intensity, volume, or length, and each has its own slider.
Select ObjectsTakes a binary layer and a table. Outputs a binary layer that contains only objects in the table.
Delete ObjectsTakes a binary layer and a table. Outputs a binary layer that excludes objects includes in the table.
Touching BordersRemoves binary objects from the layer that touch the image borders. The top and bottom faces of the z stack count, so only small objects confined to the middle frames will be preserved.
Touching FrameRemoves objects outside of a frame with the specified dimensions (the name is misleading). Can choose one of 3 options for what happens to objects touching the frame.
PlaneInserts a plane of the specified dimensions into the binary layer. Can choose which plane it is parallel to and how it affects the existing layer (Copy, which just creates a new layer; OR, which keeps the existing layer and adds the plane; AND, which keeps only portions of objects intersecting the plane; or Subtract, which removes objects overlapping with the plane).
ConnectAccording to the NIS website this node connects 2D slices from adjacent layers into 3D objects and is not necessary because other options do this automatically.
Connect CellsConnects objects that have a lot of overlap between neighboring layers and separates objects with less overlap. Has the overall effect of causing separation.
Color by IDColors objects so they can be more easily distinguished. Used this node a lot for examples above.
Color by ValueLike 2D Color by Value, color codes objects based on values from an input table. Takes some work to set up. Colored by object volume in this example.
A yellow and black background Description automatically generatedA colorful background with black border Description automatically generated with medium confidence
Renumber ObjectsLike 2D Renumber Objects, uses a binary layer from earlier in the recipe to assign objects in a new layer the same IDs they had earlier.
Renumber Using TableLike Renumber Objects but pulls ID number data from a specified column of a table.