| Name | Description | Type | Package | Framework |
| AbstractAffineTile2D | Class | mpicbg.trakem2.align | Fiji | |
| AbstractLayerAlignmentParam | Class | mpicbg.trakem2.align | Fiji | |
| AffineTile2D | Class | mpicbg.trakem2.align | Fiji | |
| Align | A collection of methods regarding SIFT-based alignment TODO Bring the methods and tasks into a class for each method and clean up this mess. | Class | mpicbg.trakem2.align | Fiji |
| Align .ExtractFeaturesThread | Extracts SIFT-features from a List of Tiles and saves them to disk. | Class | mpicbg.trakem2.align.Align | Fiji |
| Align .MatchFeaturesAndFindModelThread | Class | mpicbg.trakem2.align.Align | Fiji | |
| Align .Param | Class | mpicbg.trakem2.align.Align | Fiji | |
| Align .ParamOptimize | Class | mpicbg.trakem2.align.Align | Fiji | |
| AlignLayersTask | Register a range of layers using linear or non-linear transformations. | Class | mpicbg.trakem2.align | Fiji |
| AlignmentUtils | Class | mpicbg.trakem2.align | Fiji | |
| AlignmentUtils .ParamPointMatch | Class | mpicbg.trakem2.align.AlignmentUtils | Fiji | |
| AlignTask | Methods collection to be called from the GUI for alignment tasks. | Class | mpicbg.trakem2.align | Fiji |
| AlignTask .ReferenceData | Class | mpicbg.trakem2.align.AlignTask | Fiji | |
| BlockMatchPairCallable | Class | mpicbg.trakem2.align.concurrent | Fiji | |
| BlockMatchPairCallable .BlockMatchResults | Class | mpicbg.trakem2.align.concurrent.BlockMatchPairCallable | Fiji | |
| ElasticLayerAlignment | Class | mpicbg.trakem2.align | Fiji | |
| ElasticLayerAlignment .Param | Class | mpicbg.trakem2.align.ElasticLayerAlignment | Fiji | |
| ElasticMontage | Class | mpicbg.trakem2.align | Fiji | |
| ElasticMontage .Param | Class | mpicbg.trakem2.align.ElasticMontage | Fiji | |
| GenericAffineTile2D | Class | mpicbg.trakem2.align | Fiji | |
| RegularizedAffineLayerAlignment | Class | mpicbg.trakem2.align | Fiji | |
| RegularizedAffineLayerAlignment .Param | Class | mpicbg.trakem2.align.RegularizedAffineLayerAlignment | Fiji | |
| RigidTile2D | Class | mpicbg.trakem2.align | Fiji | |
| SimilarityTile2D | Class | mpicbg.trakem2.align | Fiji | |
| TileConfiguration | Class | mpicbg.trakem2.align | Fiji | |
| TranslationTile2D | Class | mpicbg.trakem2.align | Fiji | |
| Util | Class | mpicbg.trakem2.align | Fiji | |
| Util .Features | Class | mpicbg.trakem2.align.Util | Fiji | |
| Util .PointMatches | Class | mpicbg.trakem2.align.Util | Fiji | |