Image suite for training models for MIBI images

[manugarciaquismondo]

Greetings,

We managed to run the notebook Interior-Edge Segmentation 2D Fully Convolutional and trained a DeepCell model by using the dataset https://deepcell-data.s3.amazonaws.com/nuclei/HeLa_S3.npz.

Our aim is to use DeepCell to train a model with MIBI images. We have found that, in the webpage http://www.deepcell.org/predict, a model called mibi is available for training. Can you please provide such a model (in the form of a matrix of model weights in .h5 format) and the image suite that was used to train this model (in the form of a .npz file)?

Thank you very much,

[willgraf]

Hi,

While it is not easy for me to share the .h5 file, I can provide a notebook that walks through how we trained the MIBI model.

In regards to data, we used data that we did not generate, so I will talk with the owners of the data to see if it is OK to share.

[manugarciaquismondo]

Greetings,

Thank you for your prompt reply. Since it is not easy to share the .h5 file, can you please provide a notebook that I can use to train our MIBI model?

Thank you,