motile_plugin.example_data
Attributes
Functions
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Loads the Fluo-N2DL-HeLa 01 training raw data and silver truth from |
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Read a CTC dataset from a zarr (assumes pre-downloaded and converted) |
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Download a dataset from the Cell Tracking Challenge |
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Convert tiff file image data to zarr. Also deletes the tiffs! |
Module Contents
- motile_plugin.example_data.logger
- motile_plugin.example_data.Fluo_N2DL_HeLa() list[napari.types.LayerData]
Loads the Fluo-N2DL-HeLa 01 training raw data and silver truth from the appdir “user data dir”. Will download it from the CTC and convert it to zarr if it is not present already. Returns:
- list[LayerData]: An image layer of 01 training raw data and a labels
layer of 01 training silver truth labels
- motile_plugin.example_data.read_ctc_dataset(ds_name: str, data_dir: pathlib.Path) list[napari.types.LayerData]
Read a CTC dataset from a zarr (assumes pre-downloaded and converted) and returns a list of layer data for making napari layers
- Args:
ds_name (str): Dataset name data_dir (Path): Path to the directory containing the zarr
- Returns:
- list[LayerData]: An image layer of 01 training raw data and a labels
layer of 01 training silver truth labels
- motile_plugin.example_data.download_ctc_dataset(ds_name: str, data_dir: pathlib.Path) None
Download a dataset from the Cell Tracking Challenge and unzip it, then delete the zip. Then convert the tiffs to zarrs for the first training set images and silver truth.
- Args:
ds_name (str): Dataset name, according to the CTC data_dir (Path): The directory in which to store the data.
- motile_plugin.example_data.convert_to_zarr(tiff_path: pathlib.Path, zarr_path: pathlib.Path, zarr_group: str)
Convert tiff file image data to zarr. Also deletes the tiffs! Args:
tif_path (Path): Path to the directory containing the tiff files zarr_path (Path): path to the zarr file to write the output to zarr_group (Path): group within the zarr store to write the data to