Modules
Deprecated (not recommended) /
- Filter objects
- Binary operations (legacy)
- Merge channels
- Channel extractor
- Relate objects
- Add overlay
- Resolve co-occurrence
Hidden
Image measurements /
- Measure image texture
- Measure image dimensions
- Measure image colocalisation
- Image measurement calculator
- Measure intensity distribution
- Measure image intensity
Image processing / Pixel /
- Threshold image
- Manually edit image
- Combing correction
- Bleaching correction
- Plot kymograph
- Project image
- Invert image intensity
- Normalise intensity
- Set intensity display range
- Colour deconvolution
- Image math
- Set lookup table
- Weka probability maps
- Filter image
- Image calculator
Image processing / Pixel / Binary /
- Watershed transform
- Dilate and erode
- Fill holes
- Binary operations 2D
- Calculate distance map
- Fix skeleton breaks
- Extended minima
- Fill holes by volume
Image processing / Stack /
- Best focus stack
- Unwarp images
- Crop image
- Remove image
- Unwarp images (manual)
- Register images
- Focus stack
- Extract substack
- Apply offset correction
- Interpolate Z axis
- Image type converter
- Replace image
- Convert stack to timeseries
- Concatenate stacks
- Flip stack
Input output /
Miscellaneous /
Miscellaneous / Macros /
Object measurements / Intensity /
- Measure spot intensity
- Measure object texture
- Measure object colocalisation
- Measure object intensity
- Measure radial intensity profile
Object measurements / Miscellaneous /
- Replace measurement value
- Calculate measurement periodogram
- Object measurement calculator
- Bin objects by measurement
- Calculate statistics for children
Object measurements / Spatial /
- Measure track motion
- Measure relative orientation
- Fit ellipse
- Calculate nearest neighbour
- Measure skeleton
- Measure object shape
- Fit longest chord
- Measure object limits
- Fit ellipsoid
- Measure object curvature
- Measure object centroid
- Fit Gaussian 2D
- Measure object overlap
Object processing / Identification /
- Ridge detection
- Extract object edges
- Get local object region
- Active contour-based detection
- Run TrackMate
- Manually identify objects
- Hough-based detection
- Project objects
- Identify objects
- Track objects
Object processing / Miscellaneous /
Object processing / Refinement /
Object processing / Refinement / Filter objects /
- Remove on image edge
- Based on measurement
- Without measurement
- Objects with specific IDs
- Number of children
- With / without parent
Object processing / Refinement / Merge objects /
Object processing / Relationships /
Visualisation /
- Create measurement map
- Plot measurements as scatter
- Show image
- Create object density map
- Create orthogonal view