Comments (3)
The make_training_data
function is set to use local filepaths. /data/data/cells/ecoli/kc/set1/processed
was a local path to data that is not available.
deepcell supports downloading example data to train/predict on, and there is an issue to update the example notebooks to use this deepcell.data
instead of the local filepaths (#110 )
Ultimately, you can use the notebooks as a guide to make your own data, but currently, they reference data that was on a local machine. We are working on making these notebooks runnable for everyone.
from deepcell-tf.
Thank you for the feedback. Is there any way that you could provide us with the files required to run the example Jupyter notebooks (https://github.com/vanvalenlab/deepcell-tf/tree/master/scripts/deepcell)?
from deepcell-tf.
The referenced branch has jupyter notebooks that download data from S3 and train on that.
All users should be able to run these notebooks now without issue (once the branch is merged in).
This branch will be closed upon merge, as the issue will be resolved.
from deepcell-tf.
Related Issues (20)
- h_maxima() got an unexpected keyword argument 'footprint' HOT 7
- Nuclear size modification in script HOT 4
- CI: Test against development versions of core dependencies
- Tensorflow issue in Mesmer HOT 3
- Read the Docs build requirements change
- Incompatible shape of testing dataset in Nuclear Segmentation notebook HOT 6
- Tissuenet dataset instance segmentation ground truth HOT 11
- DEEPCELL_ACCESS_TOKEN HOT 6
- Link nucleus to whole cell segmentation mask mesmer HOT 3
- Getting cell segmentation mask file from Mesmer standalone program HOT 1
- QUERY : Segmentation Issue HOT 2
- Nuclear and whole cell segmentation masks identical HOT 4
- Question regarding pixel expansion HOT 1
- Retrieve model output without postprocessing
- Access token needed HOT 1
- Segmentation Mask Output HOT 1
- Segmentation Mask FIle Issues HOT 1
- MacBook M3 support, DeepCell cannot be installed due to tensorflow version HOT 2
- Error creating segmentation masks for small images HOT 3
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