'plates at 10,000-20,000 cells/well. The seeded cells were then '
'incubated for 1-2 hours to allow for cell adhesion to the bottom of '
'the well plate before imaging.',
'Imaging':
'Cells were imaged on a Nikon Eclipse Ti-2 fluorescence microscope at '
'20x and 40x for NIH3t3 and Raw293.6 cells respectively. The well '
'plate was placed in a Nikon incubated stage with an Oko labs '
'environment controller set to 37C and 5% CO2. Each data set was '
'generated using the Nikon jobs function to collect a z-stack of phase '
'images.'
}
#:
all_cells = Dataset(
path='all_phase_fixed.npz',
url=
'https://deepcell-data.s3-us-west-1.amazonaws.com/cytoplasm/brightfield/20190813_all_phase_512_contrast_adjusted_curated.npz',
file_hash='11f5c0cc0899905ea889463be3cd4773',
metadata={'methods': methods})
#:
nih_3t3 = Dataset(
path='nih_3t3-phase.npz',
url=
'https://deepcell-data.s3.amazonaws.com/cytoplasm/brightfield/nih_3t3-phase_fixed.npz',
file_hash='d1a3b5a548300ef8389cee8021f53957',
metadata={'methods': methods})
#:
a549 = Dataset(
path='A549-phase.npz',
url=
# limitations under the License.
# ==============================================================================
"""Builtin Datasets"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from deepcell.datasets import Dataset
# pylint: disable=line-too-long
hek293 = Dataset(
path='hek293.trks',
url='https://deepcell-data.s3.amazonaws.com/tracked/HEK293.trks',
file_hash='d5c563ab5866403836f2dcbe249c640f',
metadata={})
hela_s3 = Dataset(
path='HeLa_S3.trks',
url='https://deepcell-data.s3.amazonaws.com/tracked/HeLa_S3.trks',
file_hash='590ee37d3c703cfe029a2e60c9dc777b',
metadata={})
nih_3t3 = Dataset(
path='3T3_NIH.trks',
url='https://deepcell-data.s3.amazonaws.com/tracked/3T3_NIH.trks',
file_hash='0d90ad370e1cb9655727065ada3ded65',
metadata={})
# limitations under the License.
# ==============================================================================
"""Builtin Datasets"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from deepcell.datasets import Dataset
# pylint: disable=line-too-long
nih_3t3 = Dataset(
path='3T3_NIH.trks',
url='https://deepcell-data.s3.amazonaws.com/tracked/3T3_NIH.trks',
file_hash='0d90ad370e1cb9655727065ada3ded65',
metadata={}
)
hek293 = Dataset(
path='hek293.trks',
url='https://deepcell-data.s3.amazonaws.com/tracked/HEK293.trks',
file_hash='d5c563ab5866403836f2dcbe249c640f',
metadata={}
)
hela_s3 = Dataset(
path='HeLa_S3.trks',
url='https://deepcell-data.s3.amazonaws.com/tracked/HeLa_S3.trks',
'Cells were imaged on a Nikon Eclipse Ti-2 fluorescence microscope at '
'20x and 40x for NIH3t3 and Raw293.6 cells respectively. The well '
'plate was placed in a Nikon incubated stage with an Oko labs '
'environment controller set to 37C and 5% CO2. '
'Cytoplasm labeled with Cell Tracker CMFDA was visualized using the '
'Nikon Sola LED light source and a Semrock GFP-4050B filter cube. '
'Nuclei labeled with Hoescht 33342 were visualized with the same light '
'source and a Semrock DAPI-3060 filter cube. Each data set was '
'generated using the Nikon jobs function to image all fluorophores '
'and phase as well as a z-stack of phase images.'
}
all_cells = Dataset(
path='20190903_all_fluorescent_cyto_512.npz',
url=
'https://deepcell-data.s3-us-west-1.amazonaws.com/cytoplasm/fluorescent/20190903_all_fluorescent_cyto_512.npz',
file_hash=
'810f8180185dea6169f01470126fae4e38511645267fe92115d592ca11e1835e',
metadata={'methods': methods})
nih_3t3 = Dataset(
path='nih_3t3-cytoplasm.npz',
url=
'https://deepcell-data.s3-us-west-1.amazonaws.com/cytoplasm/fluorescent/AM_3T3_s0_fluorescent_cyto_medium_stitched_2D_512.npz',
file_hash=
'd04630d87835d27f11d80c123eac3d77684c57dadf783158c44084b11fac1fb3',
metadata={'methods': methods})
A549 = Dataset(
path='A549-cytoplasm.npz',
url=
'Cells were imaged on a Nikon Eclipse Ti-2 fluorescence microscope at '
'20x and 40x for NIH3t3 and Raw293.6 cells respectively. The well '
'plate was placed in a Nikon incubated stage with an Oko labs '
'environment controller set to 37C and 5% CO2. '
'Cytoplasm labeled with Cell Tracker CMFDA was visualized using the '
'Nikon Sola LED light source and a Semrock GFP-4050B filter cube. '
'Nuclei labeled with Hoescht 33342 were visualized with the same light '
'source and a Semrock DAPI-3060 filter cube. Each data set was '
'generated using the Nikon jobs function to image all fluorophores '
'and phase as well as a z-stack of phase images.'
}
#:
all_cells = Dataset(
path='all_fluorescent_cyto_fixed.npz',
url=
'https://deepcell-data.s3-us-west-1.amazonaws.com/cytoplasm/fluorescent/20190903_all_fluorescent_cyto_512_contrast_adjusted_curated.npz',
file_hash='6548b5b54cd940fb7ced864b4422eb96',
metadata={'methods': methods})
#:
nih_3t3 = Dataset(
path='nih_3t3-cytoplasm.npz',
url=
'https://deepcell-data.s3-us-west-1.amazonaws.com/cytoplasm/fluorescent/nih_3t3-cytoplasm_fixed.npz',
file_hash='a4e671a2c08e102f158903b288e88fff',
metadata={'methods': methods})
#:
a549 = Dataset(
path='A549-cytoplasm.npz',
url=
'plates at 10,000-20,000 cells/well. The seeded cells were then '
'incubated for 1-2 hours to allow for cell adhesion to the bottom of '
'the well plate before imaging.',
'Imaging':
'Cells were imaged on a Nikon Eclipse Ti-2 fluorescence microscope at '
'20x and 40x for NIH3t3 and Raw293.6 cells respectively. The well '
'plate was placed in a Nikon incubated stage with an Oko labs '
'environment controller set to 37C and 5% CO2. Each data set was '
'generated using the Nikon jobs function to collect a z-stack of phase '
'images.'
}
all_cell = Dataset(
path='20190813_all_phase_512.npz',
url=
'https://deepcell-data.s3-us-west-1.amazonaws.com/cytoplasm/brightfield/20190813_all_phase_512.npz',
file_hash=
'1b10bb58175461bc45ccddeaa4dc8195cc25c0a7c0ba55e25541531830a75d91',
metadata={'methods': methods})
nih_3t3 = Dataset(
path='nih_3t3-phase.npz',
url=
'https://deepcell-data.s3.amazonaws.com/cytoplasm/brightfield/AM_3T3_s0_phase_medium_stitched_2D_512.npz',
file_hash=
'b0dc7fa28d6ec4dec25150187b9629330689372da40f730042f8e0824df4da2e',
metadata={'methods': methods})
A549 = Dataset(
path='A549-phase.npz',
url=