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vanvalenlab / deepcell-tf

Deep Learning Library for Single Cell Analysis
https://deepcell.readthedocs.io
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Image suite for training models for MIBI images #157

Closed manugarciaquismondo closed 5 years ago

manugarciaquismondo commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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,