Published May 26, 2021 | Version v1
Dataset Open

Stardist model and training dataset for automated tracking of MDA-MB-231 and BT20 cells

  • 1. Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku
  • 2. Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland


StarDist Model:
The StarDist model was generated using the ZeroCostDL4Mic platform (Chamier et al., 2021). This custom StarDist model was trained for 300 epochs using 46 manually annotated paired images (image dimensions: (1024, 1024)) with a batch size of 2, an augmentation factor of 4 and a mae loss function. The StarDist “Versatile fluorescent nuclei” model was used as a training starting point. Key python packages used include TensorFlow (v 0.1.12), Keras (v 2.3.1), CSBdeep (v 0.6.1), NumPy (v 1.19.5), Cuda (v 11.0.221). The training was accelerated using a Tesla P100GPU.
The model weights can be used in the ZeroCostDL4Mic StarDist 2D notebook or in the StarDist Fiji plugin.

StarDist Training dataset:
Paired microscopy images (fluorescence) and corresponding masks

Microscopy data type: Fluorescence microscopy (SiR-DNA) and masks obtained via manual segmentation (see for details about the segmentation)

Cells were imaged using a 20x Nikon CFI Plan Apo Lambda objective (NA 0.75) one frame every 10 minutes for 16h.

Cell type: MDA-MB-231 cells and BT20 cells

File format: .tif (16-bit for fluorescence and 8 and 16-bit for the masks)



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