Galaxy | Tool Preview

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Perform segmentation of multiplexed tissue data (version 0.12.3+galaxy3)

Image containing the all marker(s):

The numerical indices of the channel(s) for the nuclear markers:

No quotes, separated by comma. e.g. 0, 1.

Resolution of the image in microns-per-pixel:

Whether to np.squeeze the outputs before saving:

Compartment for segmentation prediction: :

Whole Cell Options

Whole Cell Options 0

Mesmer

Mesmer is a DeepCell application that uses a pre-trained model for predicting nuclear and whole cell segmentation from multiplex tissue data.

Inputs 1. a multiple tissue image that includes a nuclear marker and optionally cytoplasm/membrane markers

Outputs 1. the nuclear or whole cell segmentation mask