StarDist

class byotrack.implementation.detector.stardist.StarDistDetector(model: StarDist2D | StarDist3D, **kwargs: Any)

Bases: BatchDetector

Runs stardist as a detector.

Wraps the official implementation at https://github.com/stardist/stardist, following the paper: Uwe Schmidt, Martin Weigert, Coleman Broaddus, and Gene Myers. Cell Detection with Star-convex Polygons. International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Granada, Spain, September 2018.

We do not provide any code to train the stardist model. You can only use a trained or pretrained model. We currently only wraps the 2D model of stardist.

Note

This module requires stardist lib to be installed (with tensorflow). Please follow the instruction of the official implementation to install it.

model

Underlying StarDist model

Type:: StarDist2D

prob_threshold

Threshold on probability

Type:: float

nms_threshold

Threshold for Non Maximum Suppression

Type:: float

detect(batch: ndarray) → list[Detections]

Apply the detection on a batch of frames.

By default, the frame ids are set from 0 to n-1 with n the size of the batch. The aggregattion of batches and frame ids correction is automatically handled when called the run method.

Parameters:: batch (np.ndarray) – Batch of video frames Shape: (B, [D, ]H, W, C)
Returns:: Detections for each given frame
Return type:: Sequence[byotrack.Detections]

static from_pretrained(name: str, dim=2, **kwargs: Any) → StarDistDetector

Load a pretrained StarDist from the paper.

Parameters:

name (str) – A valid identifier (From the official github)
dim (int) – Image dimension (2d or 3d). Will load the model using the correct StarDist class. Default: 2 (Use StarDist2D)
**kwargs – Additional detector arguments. (See byotrack.BatchDetector)

Returns:

StarDistDetector

static from_trained(train_dir: str | os.PathLike, dim=2, **kwargs: Any) → StarDistDetector

Load a trained StarDist from a local folder.

Parameters:

train_dir (str | os.PathLike) – The training folder of the model
dim (int) – Image dimension (2d or 3d). Will load the model using the correct StarDist class. Default: 2 (Use StarDist2D)
**kwargs – Additional detector arguments. (See byotrack.BatchDetector)

Returns:

StarDistDetector