Generic selectors
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Post Type Selectors
CleanGets rid of small noise. Built into most of the thresholding operations.
Close HolesFills small holes inside binary regions. Can choose number of iterations, used 10 here on a binary generated by Threshold with no additional postprocessing and 25 iterations.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
ComplementInverts the binary.
Fill HolesFills holes in the binary layer. Built into most of the thresholding options.
Separate ObjectsBreaks binary objects up into smaller ones. Built into most of the thresholding operations.
Separate BrightSeparates binary objects, using both binary and intensity layers. For bright objects on dark backgrounds.
Separate DarkSeparates binary objects, using both binary and intensity layers. For dark objects on bright backgrounds.
SmoothSmooths out binary objects. Built into most of the thresholding options.
OpenUses Erode then Dilate, removing small objects.
CloseUses Dilate then Erode, connecting objects and filling holes.
ErodeShrinks binary objects.
DilateExpands binary objects.
Circular OpenGets rid of binary objects under a certain radius, used 5 pixels here.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
Circular CloseFills in holes smaller than the specified radius, used 10 pixels. Effect is most obvious on single cells.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
Circular ErodeErode using a circle as its kernel instead of a matrix.
Circular DilateDilate using a circle as its kernel instead of a matrix.
Linear Open/Close/Erode/DilateOpen/close/erode/dilate using a linear matrix as its kernel. Can select matrix and number of iterations. Will result in some lines. Linear Open’s effect on a cell with 15 iterations and a horizontal matrix shown.
A yellow spot on a black background Description automatically generatedA yellow and black image Description automatically generated
ContourMakes binary objects into 1-pixel contours.
A yellow and black background Description automatically generatedA red and yellow spots on a black background Description automatically generated
CentersPuts a pixel at the center of binary objects.
CentroidsPuts a pixel at the centroid of binary objects, which differs from Centers because it takes the level of intensity underneath the binary layer into account and weights the centroid towards more intense areas. Can specify if signal is bright or dark.
Connect ObjectsConnects objects less than the specified distance apart with lines. Used 100 px (any smaller did not show an effect) and it took a VERY long time.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
Convex HullExpands concave objects to make them convex.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
Homotopic MarkingRepresents objects with single points, using a different method than center or centroid.
PruningDebranches objects made by skeletonizing functions. Can choose number of iterations.
Ultimate ErosionUses Erode until one more iteration would remove objects. Can set how many iterations to keep.
Medial AxisSeems to look for midlines of objects, result similar to skeletonizing. Increasing endlines suppression will decrease branches.
Distance FunctionUses binary and original image to create a floating point layer that shows each pixel’s distance to the background pixels.
GranulometryAdds a granulometry floating point layer, which shows the grain size of binary objects.
ThickeningUses dilate to enlarge objects but prevents them from touching each other. until objects touch each other. Increasing parameter increases how much objects grow. Used Color by ID to show how objects remain separate and 30 iterations.
Zones of InfluencePuts borders at the midpoints between objects.
A yellow and black background Description automatically generatedA red and yellow cells Description automatically generated
Fast ExoskeletonFaster algorithm for creating zones influence (but zones of influence does not have any speed issues).
A yellow and black background Description automatically generatedA close up of a cell Description automatically generated
Grow ObjectsGrows objects by specified radius but prevents them from touching. Will make objects more convex. Used 15 px here. Might be useful for making borders smoother.
A yellow and black background Description automatically generatedA yellow and black background Description automatically generated
Grow RegionsTakes a binary and color input. Extends binary objects to the specified intensity on the color layer. Can choose bright or dark regions. Used a lower threshold of 40 for bright objects. Might be useful if thresholding had to miss some parts of cells because of noise because it makes sure areas are connected to already detected objects.
A yellow object with black background Description automatically generatedA yellow spot in a black background Description automatically generated
Watershed“Floods” image starting from either bright or dark regions, taking a binary and an RGB input. Essentially the inverse of zones of influence, ended up with a layer of {1} with 1-pixel wide {0} borders between regions using from bright to dark and the same but showing cell edges using from dark to bright. Will need to use Complement to see anything useful.
A yellow and black background Description automatically generatedA close up of a colorful pattern Description automatically generated with medium confidence

From dark regions 🡪 complement

A colorful pattern with yellow lines Description automatically generated with medium confidence

From bright regions 🡪 complement

Make Inside & RingCreates 2 new binary layers from the input: the inside of objects and the border. Can also expand objects’ radius with Grow by and specify ring width. Used grow by 30 and width 10 px here.
A yellow and black background Description automatically generatedA red and blue spots on a black background Description automatically generated
SkeletonizeSkeletonizes binary objects, which preserves their general shape while removing most of the area.
A yellow and black background Description automatically generatedA black background with yellow and red spots Description automatically generated
Detect BranchingPuts single binary pixels at branch points of skeleton.
A yellow and red symbol Description automatically generatedA red and yellow lights in the sky Description automatically generated
Detect EndingsPuts single pixels at the end of branches.
A yellow and red logo Description automatically generatedA red light in the dark Description automatically generated
Cut BranchesGets rid of branches smaller than the specified length.
Connect Free EndingsUses a binary skeleton and RGB layer as inputs. Supposed to connect branches, with sensitivity determined by Connections input, but did not get it to work very well, and the algorithm was very time-consuming.
Vanish Small ObjectsGets rid of small binary skeleton objects using an RGB layer as comparison. Can specify diameter of objects to remove, as well as intensity threshold that determines if a small object is kept (because it has a high signal-noise ratio and is probably real data). Could not get it to work.
Remove Short FilamentsShortens branch ends by the specified number of pixels.
Make 4-ConnectiveChanges pixels from 8-connected (pixels touching either adjacent or diagonally) to 4-connected (adjacent pixels only considered connected) by adding some.
Make 8-ConnectiveSwitches connectivity from 4-connected to 8-connected by removing pixels.
Filter ObjectsA filter for removing binary objects that also takes an RGB layer as an input. Lots of filter options to choose from, such as diameter, convexity, area, and perimeter.
Select ObjectsTakes a table and a binary layer and selects objects that are represented in the table.
Delete ObjectsSimilar to Select Objects, but removes objects represented in the table.
(Remove Objects) Touching BordersGets rid of binary objects that touch the image border.
(Remove Objects) Touching FrameGets rid of objects the specified distance or less from the image borders. Can change mode to keep objects touching the limit or not as well as choose from units.
Insert Line/Parallel Lines/Circle/Ellipse/Rectangle/Frame/etc.Inserts a binary object. Can specify parameters/dimensions. Can also select mode: copy (deletes input layer), logical OR/AND, or subtract.
Color by IDColors the binary objects in the layer.
A yellow and black background Description automatically generatedA colorful splattered background Description automatically generated with medium confidence
Color by ValueUsing a table and a binary layer, lets you color code binary objects by parameters. To use it, you have to go into the menu and select the columns. Clicking the gear will help create value ranges. Color coded by perimeter here. A screenshot of a computer Description automatically generated
A yellow and black background Description automatically generatedA colorful splattered background Description automatically generated with medium confidence
Renumber ObjectsUsing a binary layer and a reference, reassigns object IDs in the binary layer to what they were in the reference layer. For example, if remove objects touching borders is used on a binary layer, a different object will have ID number 20 than the original layer. However, if Renumber Objects is used with the original layer as reference, the original object with ID 20 will have ID 20.
Renumber Using TableAnother node for renumbering objects to their IDs from earlier in processing but takes a binary layer and a table. Must select a column to pull object IDs from.
TMA RenumberObject numbering scheme for tissue microarray cores. Detects a square grid of cores and numbers objects based on position. Different from default binary numbering because it skips IDs of unfilled positions.
Add Borders/Crop/Change Canvas/Fit Size/Move/Resize to Ref/RotateWork like the Transformations section of preprocessing, but for a binary layer.
JS Preprocess/JS Preprocess to FloatOpen a JavaScript interface for coding your own image operations. Take RGB inputs by default but can change inputs to as many binary channels as needed. The only difference between the two is the data type of the output.