| Name | Description | Type | Package | Framework |
| Cache | Access is not synchronized, that is your duty. | Class | ini.trakem2.persistence | Fiji |
| DBLoader | Class | ini.trakem2.persistence | Fiji | |
| DBObject | Base class of all objects that can be saved in a database or XML file. | Class | ini.trakem2.persistence | Fiji |
| DownsamplerMipMaps | Class | ini.trakem2.persistence | Fiji | |
| FilePathRepair | A class to manage "file not found" problems. | Class | ini.trakem2.persistence | Fiji |
| FSLoader | A class to rely on memory only; except images which are rolled from a folder or their original location and flushed when memory is needed for more. | Class | ini.trakem2.persistence | Fiji |
| ImageBytes | Represent an image with byte arrays: 2 channels: grey + alpha | Class | ini.trakem2.persistence | Fiji |
| IntegralImageMipMaps | Class | ini.trakem2.persistence | Fiji | |
| Loader | Handle all data-related issues with a virtualization engine, including load/unload and saving, saving as and overwriting. | Class | ini.trakem2.persistence | Fiji |
| ProjectTiler | Class | ini.trakem2.persistence | Fiji | |
| StaleFiles | Methods to remove files that are no longer referenced from the current Patch instances of a Project. | Class | ini.trakem2.persistence | Fiji |
| StaleFiles .AlphaMaskPath | Class | ini.trakem2.persistence.StaleFiles | Fiji | |
| StaleFiles .CoordinateTransformPath | Class | ini.trakem2.persistence.StaleFiles | Fiji | |
| StaleFiles .Path | Interface | ini.trakem2.persistence.StaleFiles | Fiji | |
| TMLHandler | Creates the project objects from an XML file (TrakEM2 Markup Language Handler). | Class | ini.trakem2.persistence | Fiji |
| XMLOptions | Class | ini.trakem2.persistence | Fiji | |