Table 1.
ImageJ software integrations
| Software | Integration project | Supporting technologies |
|---|---|---|
| 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] | - |
* Provides cross-language interprocess integration with JavaScript, Python and others.
† Advanced Library for Integrated Development of data analysis Applications (Alida).
‡ Beaker Extensions for Jupyter (BeakerX).
§ Microscopy image analysis ToolBox (MiToBo).
¶ Open source Computer Vision library (OpenCV).
∥ REpresentational State Transfer (REST)