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.