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Application notebooks #59

Closed JLrumberger closed 1 year ago

JLrumberger commented 1 year ago

What is the purpose of this PR?

Added a notebook predict.ipynb in the style of the ark-analysis template notebooks that calculates a normalization dictionary, loads the classification model and does predictions on FOVs. The output predictions can be saved as images and plotted within the notebook and are written into a cell table that will be saved as pred_cell_table.csv.

How did you implement your changes

In this PR, all notebook specific functions are still defined in the notebook. In future versions this will be put in a python file and imported in the notebook.

Remaining issues

To import functions from the cell_classification folder, we need to add "../src" to path.

review-notebook-app[bot] commented 1 year ago

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