Just a place to put links to tutorials, software (that may be useful) etc.. This is seperate from anything to do with morphmetrics specifically (but there may be some overlap with automated landmarking)
Related CRAN task views, medical imaging, has a section on general image processing
magick - interface to imageMagick for image processing
imageR - image Processing
patternize - An R package for quantifying colour pattern variation
openCV (CV2)
scikit-image
ClearMap - ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
OMERO, Open Microscope Environment - OMERO is client-server software for managing, visualizing and analyzing microscopy images and associated metadata.
ImageJ - (java)
Fiji. (fully loaded ImageJ, java) - includes tools like TrackMate
FijiWings
CellProfiler "image processing designed for biologists"
Ilastik - Interactive learning and Image Segmentation
ImageMagick - edit, convert images (resize, etc).
A computational image analysis glossary for biologists
A tutorial for image processing in R, mostly using EMImage, including some image segmentation