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SCIP: Single-Cell Image Processing

SCIP is a software suite optimized for processing single-cell images, such as those acquired on an imaging flow cytometer. It is built on the SciJava framework, more specifically it uses the following components:

  • ImgLib2,
  • SCIFIO,
  • BioFormats,
  • ImageJ-ops,
  • ImageJ Common
  • and SciJava Common.

SCIP can be used as a plugin in ImageJ, or a as a standalone CLI.

A JAR and accompanying libraries folder can be built by cloning this repository and executing:

mvn clean package

The JAR can be run by adding the resulting target/lib and target to the Java CLASSPATH and executing:

java be.maximl.app.FeatureApp

Calling without arguments shows the usage information.