Quickstart

All non tile specific QuPath things are implemented and documented by paquo. Please refer to paquo’s documentation for these functionalities.

The focus of the package is on the use of tiles in QuPath, for example to enable a pytorch workflow. To get started with QuPath tiling in python, here are a few examples of how to use moth:

Get tiles and their annotations

The first use case of moth is to query specific tiles and the associated annotations.

Below is a small example of using moth to get the tiles and their annotations.

Open a project to work on it

The functions of moth become usable via the moth.projects.QuPathTilingProject class.

>>> from moth import QuPathTilingProject, MaskParameter
>>> qp_project = QuPathTilingProject('/path/to/project')

If a valid path was specified, the project is now opened in read only mode.

Get tile and its annotations

To retrieve tiles and their annotations just call moth.projects.QuPathTilingProject.get_tile() and moth.projects.QuPathTilingProject.get_tile_annotation_mask() methods with the desired parameters and the tile and its annotations will be returned

>>> tile = qp_project.get_tile(img_id=0, location=(50,50), size=(256,256))
>>> tilemask = qp_project.get_tile_annotation_mask(MaskParameter(img_id=0, location=(50,50)), size=(256,256))

The example shown above returns tiles and annotations for the first image at position (50|50) in size 256 x 256 pixels.

Learn more about the parameters of the functions by taking a look at the Moth API.

Save a tilemask on an image

The second use case of moth is storing generated annotations (tilemask) on images.

Open a project to work on it

To save annotations on images an existing project must be opened in non-read-only mode or a new one must be created

>>> # example: open in read/write mode
>>> from moth import QuPathTilingProject
>>> qp_project = QuPathTilingProject('/path/to/project', mode='r+')

>>> # create new project
>>> from moth import QuPathTilingProject
>>> qp_project = QuPathTilingProject('/path/to/project', mode='x')

Save tilemask

The tilemask you want to save can now be saved by calling the method moth.projects.QuPathTilingProject.save_mask_annotations()

>>> qp_project.save_mask_annotations(annotation_mask=tilemask, MaskParameter(img_id=0, location=(50,50)))

The example will save the generated tilemask in the first image starting at (50|50).

Learn more about the parameters of the function by taking a look at the Moth API.

Merge annotation

After importing multiple tile annotations, you can merge nearby annotations of the same classes. This can be done with the help of the method moth.projects.QuPathTilingProject.merge_near_annotations().

>>> qp_project.merge_near_annotations(img_id=0, max_dist=0)

This will merge all neighboring annotations that have the same class and no spacing in the first image.