Table 1 ImageJ software integrations

Apache Groovy [37]

SciJava Scripting: Groovy [101]

-

BeanShell [102]

SciJava Scripting: BeanShell [103]

-

Bio-Formats [51]

SCIFIO-Bio-Formats [104]

SCIFIO-OME-XML [105]

Bio7 (R + ImageJ 1.x) [52]

-

Eclipse [106]

CellProfiler [13]

ImageJ Server* [107]

-

ImageJ 1.x [1]

ImageJ Legacy [108]

ImageJ 1.x Patcher [109], Javassist [47]

ITK [39]

ImageJ-ITK [40]

SimpleITK [110]

JavaScript [111]

SciJava Scripting: JavaScript [112]

Nashorn [113], Rhino [114]

Jupyter Notebook [115]

SciJava Jupyter Kernel [116]

BeakerX ^‡ [117]

KNIME [15]

KNIME Image Processing [16]

-

Kotlin [118]

SciJava Scripting: Kotlin [119]

-

Lisp (JVM) [120]

SciJava Scripting: Clojure [121]

Clojure [122]

MATLAB [123]

SciJava Scripting: MATLAB [124]

matlabcontrol [125]

MATLAB

ImageJ-MATLAB [38]

SciJava Scripting: MATLAB

MiToBo ^§ [126]

-

Alida ^† [127]

OMERO [10]

ImageJ-OMERO [41]

-

OpenCV ^¶ [86]

IJ-OpenCV [128]

JavaCV [129]

Python (CPython or JVM) [130]

imglib2-imglyb [131]

pyJNIus [132], Jython [133], JyNI [134]

Python (CPython)

imagey [135]

imglib2-imglyb

Python (CPython)

SciJava Scripting: CPython [136]

javabridge [137]

Python (JVM)

SciJava Scripting: Jython [138]

Jython, JyNI

R (JVM) [139]

SciJava Scripting: Renjin [140]

Renjin [141]

REST ^∥ [142]

ImageJ Server* [107]

Dropwizard [143]

Ruby (JVM) [144]

SciJava Scripting: JRuby [145]

Ruby [144]

Scala [146]

SciJava Scripting: Scala [147]

-

TensorFlow [148]

ImageJ-TensorFlow [149]

-