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I would like to replicate the diameter calibration outside of the GUI, for the pretrained models provided. I am running:
def estimate_cell_diameters(data, channels=[2,3], gpu=False): """Estimate diameter directly using Cellpose model's size estimator""" model = Cellpose(model_type="cyto3", gpu=gpu) diams, _ = model.sz.eval(data, channels=channels) return np.maximum(5.0, diams)
This is based on the calibrate size function in the GUI, found here. Is this a reliable way of getting optimal diameters in a purely python way?
Furthermore, every time I run this function, I get different calibrated diameters. Is this expected?
The text was updated successfully, but these errors were encountered:
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I would like to replicate the diameter calibration outside of the GUI, for the pretrained models provided. I am running:
This is based on the calibrate size function in the GUI, found here. Is this a reliable way of getting optimal diameters in a purely python way?
Furthermore, every time I run this function, I get different calibrated diameters. Is this expected?
The text was updated successfully, but these errors were encountered: