deepcell.datasets¶
Basic datasets can be loaded according to the following example.
from deepcell.datasets.cytoplasm import hela
# path can be modified to determine where the dataset is stored locally
(X_train,y_train),(X_test,y_test) = hela.load_data(path='hela_cytoplasm.npz',test_size=0.1)
# Details regarding dataset collection are stored in the metadata attribute
print(hela.metadata)
Tracked datasets have a dedicated load function to handle the different data structure.
from deepcell.datasets.tracked import hela
# path can be modified to determine where the dataset is stored locally
(X_train,y_train),(X_test,y_test) = hela.load_data(path='hela_tracked.npz',test_size=0.1)
Contents
deepcell.datasets.cytoplasm¶
Fluorescent cytoplasm datasets including the raw images and ground truth segmentation masks
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deepcell.datasets.cytoplasm.
a549
= <deepcell.datasets.Dataset object>¶
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deepcell.datasets.cytoplasm.
all_cells
= <deepcell.datasets.Dataset object>¶
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deepcell.datasets.cytoplasm.
cho
= <deepcell.datasets.Dataset object>¶
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deepcell.datasets.cytoplasm.
hela
= <deepcell.datasets.Dataset object>¶
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deepcell.datasets.cytoplasm.
hela_s3
= <deepcell.datasets.Dataset object>¶
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deepcell.datasets.cytoplasm.
nih_3t3
= <deepcell.datasets.Dataset object>¶
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deepcell.datasets.cytoplasm.
pc3
= <deepcell.datasets.Dataset object>¶
deepcell.datasets.phase¶
Phase datasets including the raw images and ground truth segmentation masks
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deepcell.datasets.phase.
a549
= <deepcell.datasets.Dataset object>¶
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deepcell.datasets.phase.
all_cells
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.phase.
cho
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.phase.
hela
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.phase.
hela_s3
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.phase.
nih_3t3
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.phase.
pc3
= <deepcell.datasets.Dataset object>¶
deepcell.datasets.tracked¶
Timelapse datasets of a nuclear label including the raw images and ground truth segmentation masks annotated to track cell lineages
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deepcell.datasets.tracked.
hek293
= <deepcell.datasets.Dataset object>¶
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deepcell.datasets.tracked.
hek293_bench
= <deepcell.datasets.Dataset object>¶
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deepcell.datasets.tracked.
hela_s3
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.tracked.
hela_s3_bench
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.tracked.
nih_3t3
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.tracked.
nih_3t3_bench
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.tracked.
raw2647
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.tracked.
raw2647_bench
= <deepcell.datasets.Dataset object>¶
Module contents¶
Builtin Datasets
-
class
deepcell.datasets.
Dataset
(path, url, file_hash, metadata)[source]¶ Bases:
object
General class for downloading datasets from S3.
- Parameters
-
deepcell.datasets.
hek293
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.
hela_s3
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.
mibi
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.
mousebrain
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.
multiplex_tissue
= <deepcell.datasets.Dataset object>¶
-
deepcell.datasets.
nih_3t3
= <deepcell.datasets.Dataset object>¶