Modules
/Modules/Core
/Modules/Image measurements
- Create 2D intensity histogram
- Image measurement calculator
- Measure image colocalisation
- Measure image dimensions
- Measure image intensity
- Measure image texture
/Modules/Image processing
/Modules/Image processing/Miscellaneous
/Modules/Image processing/Pixel
- Apply CLAHE
- Bleaching correction
- Colour deconvolution
- Combing correction
- Filter image
- Image calculator
- Image math
- Invert image intensity
- Manually edit image
- Normalise intensity
- Project image
- Weka probability maps
- White balance correction
/Modules/Image processing/Pixel/Binary
- Binary operations (legacy)
- Binary operations 2D
- Dilate and erode
- Calculate distance map
- Extended minima/maxima
- Fill holes
- Fill holes by volume
- Fix skeleton breaks
- Skeletonise
- Watershed transform
/Modules/Image processing/Pixel/Threshold
/Modules/Image processing/Stack
- Apply offset correction
- Best focus stack
- Channel extractor
- Concatenate stacks
- Convert 3D stack (switch Z and T)
- Crop image
- Extract substack
- Flip stack
- Focus stack
- Image type converter
- Interpolate Z axis
- Merge channels
- Register images
- Remove image
- Replace image
/Modules/Image processing/Stack/Registration
- Affine (block matching)
- Affine (object centroids)
- Affine (MOPS)
- Affine (manual)
- Affine (SIFT)
- Unwarp (automatic)
- Unwarp (manual)
/Modules/Input output
/Modules/Miscellaneous
/Modules/Miscellaneous/Macros
/Modules/Object measurements
/Modules/Object measurements/Intensity
- Measure intensity along path
- Measure object colocalisation
- Measure object intensity
- Measure object texture
- Measure spot intensity
/Modules/Object measurements/Miscellaneous
- Apply Weka object classification
- Bin objects by measurement
- Calculate statistics for children
- Calculate statistics for partners
- Child object count
- Object measurement calculator
- Object timepoint
- Parent object ID
- Partner object count
- Replace measurement value
/Modules/Object measurements/Spatial
- Calculate nearest neighbour
- Fit ellipse
- Fit ellipsoid
- Fit Gaussian 2D
- Fit longest chord
- Fit spline
- Measure object centroid
- Measure object curvature
- Measure object limits
- Measure object overlap
- Measure object shape
- Measure relative orientation
- Measure skeleton
- Measure specific width
- Measure track motion
/Modules/Object processing
/Modules/Object processing/Identification
- Convex hull 2D
- Active contour-based detection
- Circle detection
- Extract object cross section
- Extract object edges
- Get local object region
- Get object surface
- Identify objects
- Manually identify objects
- Project objects
- Ridge detection
- Run TrackMate
- Sphere detection
/Modules/Object processing/Miscellaneous
/Modules/Object processing/Refinement
- Combine object sets
- Expand and shrink objects
- Fill holes in objects
- Mask objects
- Reassign enclosed objects
- Remove objects
- Track editor
/Modules/Object processing/Refinement/Filter objects
- Number of children
- Based on measurement
- Measurement extremes
- Number of partners
- Object proximity
- Filter objects
- Remove on image edge
- Objects with specific IDs
- With / without measurement
- With / without parent
/Modules/Object processing/Refinement/Merge objects
/Modules/Object processing/Relationships
- Relate many-to-many
- Relate many-to-one
- Relate objects
- Relate one-to-one
- Single class cluster
- Track objects
/Modules/Visualisation
- Create measurement map
- Create object density map
- Create orthogonal view
- Plot measurements as scatter
- Show image
- Show image measurements
- Show metadata
- Show object measurements
/Modules/Visualisation/ImageRendering
/Modules/Visualisation/Overlays
- Add all object points
- Add arrows
- Add contour lines
- Add from position measurement
- Add labels
- Add line
- Add object centroid
- Add object fill
- Add object outline
- Add overlay
- Add relationship connection
- Add text
- Add tracks