Modules
Deprecated (not recommended) /
General
Image measurements /
- Measure image colocalisation
- Image measurement calculator
- Measure image dimensions
- Measure image texture
- Measure image intensity
- Measure intensity distribution
Image processing / Miscellaneous /
Image processing / Pixel /
- Plot kymograph
- Filter image
- Project image
- Combing correction
- Set intensity display range
- Weka probability maps
- Threshold image
- Invert image intensity
- Bleaching correction
- Colour deconvolution
- Set lookup table
- Image math
- Image calculator
- Normalise intensity
- Manually edit image
Image processing / Pixel / Binary /
- Watershed transform
- Fill holes by volume
- Extended minima
- Fill holes
- Binary operations 2D
- Dilate and erode
- Calculate distance map
Image processing / Stack /
- Extract substack
- Best focus stack
- Flip stack
- Focus stack
- Crop image
- Interpolate Z axis
- Convert stack to timeseries
- Replace image
- Remove image
- Register images
- Unwarp images (manual)
- Image type converter
- Unwarp images
- Concatenate stacks
- Apply offset correction
Input output /
Miscellaneous /
Object measurements / Intensity /
- Measure object colocalisation
- Measure object intensity
- Measure radial intensity profile
- Measure object texture
- Measure spot intensity
Object measurements / Miscellaneous /
- Object measurement calculator
- Calculate measurement periodogram
- Calculate statistics for children
- Bin objects by measurement
Object measurements / Spatial /
- Measure track motion
- Measure object shape
- Measure object overlap
- Fit ellipsoid
- Measure object limits
- Measure object curvature
- Measure relative orientation
- Fit ellipse
- Measure object centroid
- Calculate nearest neighbour
- Fit longest chord
- Fit Gaussian 2D
Object processing / Identification /
- Active contour-based detection
- Extract object edges
- Relate objects
- Hough-based detection
- Manually identify objects
- Identify objects
- Run TrackMate
- Track objects
- Get local object region
- Project objects
- Ridge detection
Object processing / Miscellaneous /
Object processing / Refinement /
- Filter objects
- Object clustering
- Reassign enclosed objects
- Merge tracks
- Merge objects
- Expand and shrink objects
- Remove objects
Object processing / Refinement / Filter objects /
Visualisation /
- Create orthogonal view
- Create object density map
- Show image
- Create measurement map
- Plot measurements as scatter