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GitHub / Genentech / spex

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fspex

Stars: 1
Forks: 3
Open Issues: 0

License: mit
Language: PLpgSQL
Repo Size: 39.2 MB
Dependencies: 369

Created: over 1 year ago
Updated: about 2 months ago
Last pushed: about 2 months ago
Last synced: about 2 months ago

Files

Readme

Dependencies

demo_data/arango_demo/Dockerfile docker

arangodb 3.7.7 build

demo_data/omero_demo/database/Dockerfile docker

postgres 11 build

demo_data/omero_demo/omeroserver/Dockerfile docker

openmicroscopy/omero-server 5 build

demo_data/scripts/segmentation/Pipfile pypi

absl-py ==0.12.0
aicsimageio ==3.3.4
aicspylibczi ==2.8.0
alabaster ==0.7.12
jupyter *
matplotlib *
numpy *
pandas *
scikit-image ==0.18.1
scikit-learn *
tifffile *
watershed *

docker-compose-demo.yml docker

ghcr.io/genentech/spex.arango latest
ghcr.io/genentech/spex.backend latest
ghcr.io/genentech/spex.frontend latest
ghcr.io/genentech/spex.job.manager latest
ghcr.io/genentech/spex.omero.image.downloader latest
ghcr.io/genentech/spex.omero.postgresql latest
ghcr.io/genentech/spex.omero.server latest
ghcr.io/genentech/spex.omero.sessions latest
ghcr.io/genentech/spex.pipeline.manager latest
ghcr.io/genentech/spex.redis latest
openmicroscopy/omero-web-standalone 5

demo_data/scripts/segmentation/requirements.txt pypi

Cython ==3.0.0a8
DeepCell ==0.9.0
DeepCell-Tracking ==0.3.1
Deepcell-Toolbox ==0.10.1
HeapDict ==1.0.1
Keras ==2.3.1
Keras-Applications ==1.0.8
Keras-Preprocessing ==1.1.2
Markdown ==3.3.4
PyOpenGL ==3.1.5
PyQt5 ==5.15.4
PyQt5-Qt5 ==5.15.2
PyQt5-sip ==12.8.1
PyYAML ==5.4.1
QtPy ==1.9.0
Send2Trash ==1.5.0
Sphinx ==3.5.4
Werkzeug ==1.0.1
absl-py ==0.12.0
aicsimageio ==3.3.4
aicspylibczi ==2.8.0
alabaster ==0.7.12
appdirs ==1.4.4
astunparse ==1.6.3
async-generator ==1.10
brotlipy ==0.7.0
cachetools ==4.2.1
cachey ==0.2.1
cellpose ==0.6.5
certifi ==2020.12.5
click ==7.1.2
csbdeep ==0.6.1
cycler ==0.10.0
cytoolz ==0.11.0
distributed ==2021.4.1
docstring-parser ==0.7.3
docutils ==0.16
flatbuffers ==1.12
freetype-py ==2.2.0
gast ==0.4.0
google-auth ==1.29.0
google-auth-oauthlib ==0.4.4
google-pasta ==0.2.0
graphviz ==0.8.4
grpcio ==1.34.1
h5py ==2.10.0
imagesize ==1.2.0
ipywidgets ==8.0.0a5
joblib ==1.0.1
jupyter ==1.0.0
jupyter-console ==6.4.0
jupyter-resource-usage ==0.6.0
jupyterlab-system-monitor ==0.8.0
jupyterlab-topbar ==0.6.1
jupyterlab-widgets ==2.0.0a2
keras-nightly ==2.5.0.dev2021032900
llvmlite ==0.36.0
locket ==0.2.1
lxml ==4.6.3
magicgui ==0.2.9
matplotlib *
mkl-fft ==1.3.0
mkl-service ==2.3.0
msgpack ==1.0.2
mxnet-mkl ==1.6.0
napari ==0.4.7
napari-console ==0.0.3
napari-plugin-engine ==0.1.9
napari-svg ==0.1.4
natsort ==7.1.1
numba ==0.53.1
numpy *
numpydoc ==1.1.0
oauthlib ==3.1.0
olefile ==0.46
opencv-python ==4.5.1.48
opencv-python-headless ==4.5.2.54
opt-einsum ==3.3.0
pandas *
pandocfilters ==1.4.2
parso ==0.7.0
pathlib ==1.0.1
protobuf ==3.15.8
psutil ==5.8.0
pyasn1 ==0.4.8
pyasn1-modules ==0.2.8
pydantic ==1.8.1
pydot ==1.4.2
pyzmq ==20.0.0
qtconsole ==5.0.3
readlif ==0.6.1
requests-oauthlib ==1.3.0
rsa ==4.7.2
scikit-image *
scikit-learn *
snowballstemmer ==2.1.0
sortedcontainers ==2.3.0
sphinxcontrib-applehelp ==1.0.2
sphinxcontrib-devhelp ==1.0.2
sphinxcontrib-htmlhelp ==1.0.3
sphinxcontrib-jsmath ==1.0.1
sphinxcontrib-qthelp ==1.0.3
sphinxcontrib-serializinghtml ==1.1.4
stardist ==0.6.2
tblib ==1.7.0
tensorboard ==2.5.0
tensorboard-data-server ==0.6.0
tensorboard-plugin-wit ==1.8.0
tensorflow ==2.5.0rc1
tensorflow-estimator ==2.5.0rc0
termcolor ==1.1.0
testpath ==0.4.4
threadpoolctl ==2.1.0
tifffile *
torch ==1.9.0
tqdm ==4.60.0
vispy ==0.6.6
webencodings ==0.5.1
widgetsnbextension ==4.0.0a3
wrapt ==1.12.1
zict ==2.0.0

demo_data/scripts/spatial_transcriptomics/environment.yml pypi

adjusttext ==1.0.4
aiobotocore ==2.5.4
aioitertools ==0.11.0
backoff ==2.2.1
blessed ==1.20.0
boto3 ==1.34.40
botocore ==1.34.40
chex ==0.1.7
click-plugins ==1.1.1
cligj ==0.7.2
colorcet ==3.0.1
contextlib2 ==21.6.0
croniter ==1.4.1
datashader ==0.16.0
dateutils ==0.6.12
decoupler ==1.4.0
deepdiff ==6.7.1
demuxem ==0.1.7
dm-tree ==0.1.8
docopt ==0.6.2
editor ==1.6.6
etils ==1.6.0
fastapi ==0.109.2
fiona ==1.9.5
flax ==0.7.4
fsspec ==2023.6.0
geopandas ==0.14.3
hnswlib ==0.8.0
igraph ==0.9.10
inquirer ==3.2.3
itsdangerous ==2.1.2
jax ==0.4.14
jaxlib ==0.4.14
jaxtyping ==0.2.21
jmespath ==1.0.1
leidenalg ==0.8.10
lightgbm ==4.3.0
lightning ==2.0.9.post0
lightning-cloud ==0.5.64
loompy ==3.0.7
ml-collections ==0.1.1
ml-dtypes ==0.3.2
mudata ==0.2.3
multipledispatch ==1.0.0
multiscale-spatial-image ==0.11.2
numpy ==1.23.4
numpy-groupies ==0.10.2
numpyro ==0.13.2
ome-zarr ==0.8.3
optax ==0.1.9
orbax-checkpoint ==0.5.3
ordered-set ==4.1.0
param ==2.0.2
pegasus ==0.1.3
pegasusio ==0.8.1
pegasuspy ==1.8.0
pybind11 ==2.11.1
pyct ==0.5.0
pydantic ==2.1.1
pydantic-core ==2.4.0
pygeos ==0.14
pyproj ==3.6.1
python-multipart ==0.0.9
pytorch-lightning ==2.0.6
readchar ==4.0.5
retrying ==1.3.4
runs ==1.2.2
s3fs ==2023.6.0
s3transfer ==0.10.0
scikit-image ==0.20.0
scikit-misc ==0.3.1
scvi-tools ==1.0.3
shapely ==2.0.2
sparse ==0.15.1
spatial-image ==0.3.0
spatialdata ==0.0.15
spatialpandas ==0.4.8
squidpy ==1.3.0
starlette ==0.36.3
starsessions ==1.3.0
tensorstore ==0.1.53
torchmetrics ==1.0.3
typeguard ==4.1.5
urllib3 ==1.26.18
uvicorn ==0.27.1
websockets ==12.0
wordcloud ==1.9.3
xarray ==2023.12.0
xarray-dataclasses ==1.7.0
xarray-datatree ==0.0.14
xarray-schema ==0.0.3
xarray-spatial ==0.3.7
xlsxwriter ==3.1.9
xmod ==1.8.1

demo_data/scripts/segmentation/Pipfile.lock pypi

128 dependencies