Modules
.Deprecated (not recommended) /
- Add overlay
- Binary operations (legacy)
- Channel extractor
- Filter objects
- Merge channels
- Relate objects
- Resolve co-occurrence
- Threshold image
.Image measurements /
- Image measurement calculator
- Measure image colocalisation
- Measure image dimensions
- Measure image intensity
- Measure image texture
- Measure intensity distribution
.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
- Plot kymograph
- Project image
- Weka probability maps
- White balance correction
.Image processing / .Pixel / .Binary /
- Binary operations 2D
- Dilate and erode
- Calculate distance map
- Extended minima
- Fill holes
- Fill holes by volume
- Fix skeleton breaks
- Skeletonise
- Watershed transform
.Image processing / .Pixel / .Threshold /
.Image processing / .Stack /
- Apply offset correction
- Best focus stack
- Concatenate stacks
- Convert 3D stack (switch Z and T)
- Crop image
- Extract substack
- Flip stack
- Focus stack
- Image type converter
- Interpolate Z axis
- Unwarp images (manual)
- Register images
- Remove image
- Replace image
- Unwarp images
.Input output /
.Miscellaneous /
.Miscellaneous / .Macros /
.Object measurements / .Intensity /
- Measure object colocalisation
- Measure object intensity
- Measure object texture
- Measure radial intensity profile
- Measure spot intensity
.Object measurements / .Miscellaneous /
- Bin objects by measurement
- Calculate measurement periodogram
- Calculate statistics for children
- Calculate statistics for partners
- Object measurement calculator
- Replace measurement value
.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
.Object processing / .Identification /
- Convex hull 2D
- Active contour-based detection
- Extract object edges
- Get local object region
- Get object surface
- Hough-based detection
- Identify objects
- Manually identify objects
- Project objects
- Ridge detection
- Run TrackMate
.Object processing / .Miscellaneous /
.Object processing / .Refinement /
- Combine object sets
- Duplicate objects across time
- Expand and shrink objects
- Mask objects
- Reassign enclosed objects
- Remove objects
.Object processing / .Refinement / .Filter objects /
- Number of children
- Based on measurement
- Measurement extremes
- Number of partners
- Remove on image edge
- Objects with specific IDs
- With / without measurement
- With / without parent
.Object processing / .Refinement / .Merge objects /
.Object processing / .Relationships /
.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
.Visualisation / .Image rendering /
.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 relationship connection
- Add text
- Add tracks