steinbock.segmentation

cellprofiler special

cellprofiler

create_and_save_segmentation_pipeline(segmentation_pipeline_file)

Source code in steinbock/segmentation/cellprofiler/cellprofiler.py

def create_and_save_segmentation_pipeline(
    segmentation_pipeline_file: Union[str, PathLike]
):
    shutil.copyfile(
        _segmentation_pipeline_file_template, segmentation_pipeline_file
    )

run_object_segmentation(cellprofiler_binary, segmentation_pipeline_file, probabilities_dir, mask_dir, cellprofiler_plugin_dir=None)

Source code in steinbock/segmentation/cellprofiler/cellprofiler.py

def run_object_segmentation(
    cellprofiler_binary: Union[str, PathLike],
    segmentation_pipeline_file: Union[str, PathLike],
    probabilities_dir: Union[str, PathLike],
    mask_dir: Union[str, PathLike],
    cellprofiler_plugin_dir: Union[str, PathLike, None] = None,
):
    args = [
        str(cellprofiler_binary),
        "-c",
        "-r",
        "-p",
        str(segmentation_pipeline_file),
        "-i",
        str(probabilities_dir),
        "-o",
        str(mask_dir),
    ]
    if cellprofiler_plugin_dir is not None:
        args.append("--plugins-directory")
        args.append(str(cellprofiler_plugin_dir))
    return run_captured(args)

deepcell

deepcell_available

Application

MESMER

run_object_segmentation(img_files, application, model=None, channelwise_minmax=False, channelwise_zscore=False, channel_groups=None, aggr_func=<function mean at 0x7f51de7e60d0>, **predict_kwargs)

Source code in steinbock/segmentation/deepcell.py

def run_object_segmentation(
    img_files: Sequence[Union[str, PathLike]],
    application: Application,
    model: Optional["Model"] = None,
    channelwise_minmax: bool = False,
    channelwise_zscore: bool = False,
    channel_groups: Optional[np.ndarray] = None,
    aggr_func: Callable[[np.ndarray], np.ndarray] = np.mean,
    **predict_kwargs,
) -> Generator[Tuple[Path, np.ndarray], None, None]:
    app, predict = application.value(model=model)
    for img_file in img_files:
        img = io.read_image(img_file)
        if channelwise_minmax:
            channel_mins = np.nanmin(img, axis=(1, 2), keepdims=True)
            channel_maxs = np.nanmax(img, axis=(1, 2), keepdims=True)
            img = (img - channel_mins) / (channel_maxs - channel_mins)
        if channelwise_zscore:
            channel_means = np.nanmean(img, axis=(1, 2), keepdims=True)
            channel_stds = np.nanstd(img, axis=(1, 2), keepdims=True)
            img = (img - channel_means) / channel_stds
        if channel_groups is not None:
            img = np.stack(
                [
                    aggr_func(img[channel_groups == channel_group], axis=0)
                    for channel_group in np.unique(channel_groups)
                    if not np.isnan(channel_group)
                ]
            )
        mask = predict(img, **predict_kwargs)
        yield Path(img_file), mask
        del img, mask