StarDist Adipocyte Segmentation Training data, Training Notebook and Model
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Data from H&E human bone marrow whole slide scanner images used in the paper: "MarrowQuant 2.0: a digital pathology workflow assisting bone marrow evaluation in clinical and experimental hematology" (https://doi.org/10.21203/rs.3.rs-1860140/v1) 292 image patches Ground truth were manually annotated using QuPath and split into 263 images for training and 29 for validation. Training in StarDist was done on a Windows 10 PC with an RTX 2080 GPU. The requirements file for installing a Python 3.7 environment to run the attached notebooks is provided (<strong>stardist-val.txt</strong>). The StarDist model configuration can be found in the Jupyter Notebook : <pre><code>Adipocyte Training.ipynb</code></pre> Model validation and metrics can be performed by running the notebook after finishing the <strong>Adipocyte Training</strong> notebook. <pre><code>Quality Control.ipynb</code></pre>
