Classic Image Processing (CIP)

CIP is a Java library focused in Image processing. It exposes Classic Image Processing functions in a convenient way for scripting, more specifically it is thought to be used in ImageJ script editor. It could be a good entry point to start scripting image analysis workflow and aim in general at easing prototyping. CIP tries to reach that goal by doing the following:

• Maintaining a carefully curated list of functions

  • Select functions already adopted by the community
  • Provide minimal set of functions to go from Image to measures
  • All functions works in 2D/3D (and nD whenever possible)
  • Aim to be on par with IJ1 speed-wise (and faster whenever possible)

• Easing functions discovery and learning

  • Consistent functions interfaces
  • Optional and named parameters
  • Strong documentation

• Making scripting easier to write and understand

  • Minimize the number of types to manipulate
  • Handling image types and conversion behind the scene
  • Minimizing library imports
  • Never modify function input

• Rely on existing infrastructure to allow CIP working hand in hand with imageJ ecosystem

  • Rely on ImgLib2 and ImageJ Op
  • Handling conversion to IJ1 and IJ2 image and regions

Aimed functionalities

Filters	Segmentation	Image wrangling	Image Math	Misc
gaussian blur	manual threshold	concatenate	add	region
erosion	auto threshold	duplicate	sub	IJ1 converters
dilation	maxima	slice	multiply	IJ2 converters
opening	extended maxima	project	divide	show
closing	multiscale maxima		logic operators	measures
tophat	binary watershed		comparison
distance map	gray level watershed		sin, cos, ...
median	seeded watershed		pow, sqrt
gradient	edge detection		floor, ceil, round
laplacian	skeletonisation		log, exp
hessian
Fillholes

Items in bold font have an implementation

Installation

to compile CIP source code

1. Clone ImgAlgo Repository
2. Import it as a Maven project in your IDE
3. Maven install the project
4. Clone CIP repository
5. import it as a Maven project in your IDE
6. compile as Maven project

to use CIP in ImageJ

CIP and ImgAlgo jar will be soon available via an ImageJ update site soon

1. Drop the ImgAlgo and CIP jar in your ImageJ plugins folder
2. Restart ImageJ
3. Open ImageJ script editor
4. Choose a language (For instance Python)
5. Add the annotation #@CIP cip at the beginning of the script
6. the variable cip is now available in the script and allows one to call any of CIP functionalities