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Usable model for cell counts of cytoplasmic IHC stains. This model's MAE is ~70. [WIP]

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jeffock/ihc_cellcount_cytoplasmic

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Reults from current model:


Annotated cell count: 62


original heatmap


Predicted cell count: 60


model heatmap


Original image: cytokeratin 14 (KRT14) stain


original image


Annotated cell count: 349


original heatmap


Predicted cell count: 507


model heatmap


Original image: cytokeratin 5 (KRT5) stain


original image


Current model is 600epoch_KRTmodel_02_shuffle.pth.tar

Step-by-Step:


git clone <url> to download the repository where url is this repo's url.

(figure out how to implement make_dataset.ipynb here)

Add the .jpg files to Data/images/ and the .h5 & .mat files to Data/ground_truth/.

A usable version without the need for annotated .mat files will be released when proper results are attained.

Run through val.ipynb while editing file paths as needed. This will return the results.

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Usable model for cell counts of cytoplasmic IHC stains. This model's MAE is ~70. [WIP]

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