Segmentation Prediction Type in online version does not have equivalent notebook application

[joshuagohos]

I can't find the notebook ipynb application that is equivalent to DeepCell Predict, for Prediction Type Segmentation.

I used DeepCell Predict online with these settings:

This yielded a good segmentation that I viewed using DeepCell Label:

I would like to obtain this same segmentation and cell labels using Jupyter notebook. Looking through the Github for ~/deepcell-tf/notebooks/applications/ I see three ipynbs. It seems to me that the Segmentation prediction type that is available in the online should be the Cytoplasm-Application.ipynb (I looked through Mesmer and Nuclear, but those seem to be for the Mesmer and maybe Caliban prediction types, respectively, online).

Giving Cytoplasm-Application.ipynb a try, this is the labeling I get:

Which is way off. Am I using the wrong application, using this application wrongly, or is there currently no ipynb equivalent for the Segmentation prediction type that is online?

[joshuagohos]

An update. I tried the Nuclear-Application.ipynb, and it seemed to do much better:

But this result is still not exactly the same as the segmentation I get from the online version (see above comment DeepCell Label figure). Moreover, in the online version, I get 376 cells. But using the Nuclear-Application.ipynb approach, I get y_pred.max() = 215.

Is the online version different from the application version used when trying to run it locally using ipynb?