| Name | Description | Type | Package | Framework |
| Apply_Transformation | Class | spim.fiji.plugin | Fiji | |
| ApplyParameters | Class | spim.fiji.plugin.apply | Fiji | |
| BigDataViewerTransformationWindow | Class | spim.fiji.plugin.apply | Fiji | |
| Data_Explorer | Class | spim.fiji.plugin | Fiji | |
| Define_Bounding_Box | Class | spim.fiji.plugin | Fiji | |
| Define_Multi_View_Dataset | Class | spim.fiji.plugin | Fiji | |
| DifferenceOf | Class | spim.fiji.plugin.interestpointdetection | Fiji | |
| DifferenceOfGaussian | Class | spim.fiji.plugin.interestpointdetection | Fiji | |
| DifferenceOfMean | Class | spim.fiji.plugin.interestpointdetection | Fiji | |
| Display_View | Class | spim.fiji.plugin | Fiji | |
| Duplicate_Transformation | Class | spim.fiji.plugin | Fiji | |
| Fusion | Class | spim.fiji.plugin.fusion | Fiji | |
| Generic_Resave_HDF5 | Class | spim.fiji.plugin.resave | Fiji | |
| Generic_Resave_HDF5 .Parameters | Class | spim.fiji.plugin.resave.Generic_Resave_HDF5 | Fiji | |
| GenericDialogAppender | Interface | spim.fiji.plugin.util | Fiji | |
| GenericLoadParseQueryXML | Interface for interactive parsing of spimdata XMLsAuthor:Stephan Preibisch (stephan. | Class | spim.fiji.plugin.queryXML | Fiji |
| GUIHelper | Class | spim.fiji.plugin.util | Fiji | |
| Histogram | Class | spim.fiji.plugin.thinout | Fiji | |
| Image_Fusion | Class | spim.fiji.plugin | Fiji | |
| Interactive_Remove_Detections | Class | spim.fiji.plugin | Fiji | |
| InteractiveProjections | Class | spim.fiji.plugin.removedetections | Fiji | |
| Interest_Point_Detection | Plugin to detect interest points, store them on disk, and link them into the XML Different plugins to detect interest points are supported, needs to implement the | Class | spim.fiji.plugin | Fiji |
| Interest_Point_Registration | Class | spim.fiji.plugin | Fiji | |
| Interest_Point_Registration .RegistrationType | Class | spim.fiji.plugin.Interest_Point_Registration | Fiji | |
| InterestPointDetection | Class | spim.fiji.plugin.interestpointdetection | Fiji | |
| InterestPointRegistration | Class | spim.fiji.plugin.interestpointregistration | Fiji | |
| LoadParseQueryXML | Class | spim.fiji.plugin.queryXML | Fiji | |
| Max_Project | Class | spim.fiji.plugin | Fiji | |
| Merge_Cluster_Jobs | Class | spim.fiji.plugin | Fiji | |
| MergeClusterJobs | Class | spim.fiji.plugin.cluster | Fiji | |
| ModelLink | Class | spim.fiji.plugin.apply | Fiji | |
| MouseListenerValue | Class | spim.fiji.plugin.thinout | Fiji | |
| MyMultiLineLabel | Class | spim.fiji.plugin.util | Fiji | |
| OpenImg | Class | spim.fiji.plugin.util | Fiji | |
| PluginHelper | Class | spim.fiji.plugin.resave | Fiji | |
| PluginHelper .ChooseXmlFileListener | Class | spim.fiji.plugin.resave.PluginHelper | Fiji | |
| ProgressWriterIJ | Class | spim.fiji.plugin.resave | Fiji | |
| Resave_HDF5 | Class | spim.fiji.plugin.resave | Fiji | |
| Resave_TIFF | Class | spim.fiji.plugin.resave | Fiji | |
| Resave_TIFF .Parameters | Class | spim.fiji.plugin.resave.Resave_TIFF | Fiji | |
| Specify_Calibration | Class | spim.fiji.plugin | Fiji | |
| Specify_Calibration .Cal | Class | spim.fiji.plugin.Specify_Calibration | Fiji | |
| ThinOut_Detections | Class | spim.fiji.plugin | Fiji | |
| Toggle_Cluster_Options | Class | spim.fiji.plugin | Fiji | |
| Visualize_Detections | Class | spim.fiji.plugin | Fiji | |
| Visualize_Detections .Params | Class | spim.fiji.plugin.Visualize_Detections | Fiji | |