| Name | Description | Type | Package | Framework |
| BinaryInterpolation2D | Given two binary images of the same dimensions, generate an interpolated image that sits somewhere | Class | ini.trakem2.imaging | Fiji |
| Blending | Utility functions for blending images together, to remove contrast seams. | Class | ini.trakem2.imaging | Fiji |
| ContrastEnhancerWrapper | Class | ini.trakem2.imaging | Fiji | |
| ContrastPlot | Copied and modified from Wayne Rasband's ImageJ ContrastPlot inner class in ij. | Class | ini.trakem2.imaging | Fiji |
| CorrectBackground | Class | ini.trakem2.imaging.filters | Fiji | |
| DefaultMinAndMax | Sets the minimum to zero and the maximum to the maximum supported, or 255 for FloatProcessor and any other unknown ImageProcessor. | Class | ini.trakem2.imaging.filters | Fiji |
| EnhanceContrast | Uses the @{link ContrastEnhancer. | Class | ini.trakem2.imaging.filters | Fiji |
| EqualizeHistogram | Class | ini.trakem2.imaging.filters | Fiji | |
| FastIntegralImage | Written following the code in ImgLib1's IntegralImage2 and ScaleAreaAveraging2d, authored by Stephan Preibisch and Albert Cardona. | Class | ini.trakem2.imaging | Fiji |
| FilterEditor | Class | ini.trakem2.imaging.filters | Fiji | |
| FloatProcessorT2 | Class | ini.trakem2.imaging | Fiji | |
| GaussianBlur | Smooth with a Gaussian. | Class | ini.trakem2.imaging.filters | Fiji |
| IFilter | Interface | ini.trakem2.imaging.filters | Fiji | |
| ImagePreprocessor | Any class implementing this interface is suitable as an image preprocessor for a TrakEM2 project. | Interface | ini.trakem2.imaging | Fiji |
| IntegralHistogram2d | An integral histogram for 2d images. | Class | ini.trakem2.imaging | Fiji |
| Invert | Class | ini.trakem2.imaging.filters | Fiji | |
| LayerStack | This class represents an entire LayerSet of Patch objects only, as it is presented read-only to ImageJ. | Class | ini.trakem2.imaging | Fiji |
| LazyVirtualStack | Class | ini.trakem2.imaging | Fiji | |
| LUTBlue | Class | ini.trakem2.imaging.filters | Fiji | |
| LUTCustom | Class | ini.trakem2.imaging.filters | Fiji | |
| LUTCyan | Class | ini.trakem2.imaging.filters | Fiji | |
| LUTGreen | Class | ini.trakem2.imaging.filters | Fiji | |
| LUTMagenta | Class | ini.trakem2.imaging.filters | Fiji | |
| LUTOrange | Class | ini.trakem2.imaging.filters | Fiji | |
| LUTRed | Class | ini.trakem2.imaging.filters | Fiji | |
| LUTYellow | Class | ini.trakem2.imaging.filters | Fiji | |
| Normalize | Class | ini.trakem2.imaging.filters | Fiji | |
| NormalizeLocalContrast | Class | ini.trakem2.imaging.filters | Fiji | |
| P | Class | ini.trakem2.imaging | Fiji | |
| PatchStack | Assumed is all Patch instances in the array are of the same size, live in consecutive layers of the same thickness. | Class | ini.trakem2.imaging | Fiji |
| PhaseCorrelationCalculator | Class | ini.trakem2.imaging | Fiji | |
| RankFilter | Class | ini.trakem2.imaging.filters | Fiji | |
| ResetMinAndMax | Class | ini.trakem2.imaging.filters | Fiji | |
| RobustNormalizeLocalContrast | Class | ini.trakem2.imaging.filters | Fiji | |
| Segmentation | Class | ini.trakem2.imaging | Fiji | |
| Segmentation .BlowCommander | Class | ini.trakem2.imaging.Segmentation | Fiji | |
| Segmentation .BlowRunner | Class | ini.trakem2.imaging.Segmentation | Fiji | |
| Segmentation .FastMarchingParam | Class | ini.trakem2.imaging.Segmentation | Fiji | |
| StitchingTEM | - known percent overlap This class will attempt to find the optimal montage, | Class | ini.trakem2.imaging | Fiji |
| StitchingTEM .PhaseCorrelationParam | Class | ini.trakem2.imaging.StitchingTEM | Fiji | |
| SubtractBackground | Subtract background with the rolling-ball algorithm. | Class | ini.trakem2.imaging.filters | Fiji |
| ValueToNoise | Class | ini.trakem2.imaging.filters | Fiji | |