vanvalenlab

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34 repositories

intro-to-deepcell
Public archive
An introduction to deepcell and deep learning
Jupyter Notebook
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Other
•26•141•8•0•Updated Oct 21, 2024Oct 21, 2024
deepcell-tf
Public
Deep Learning Library for Single Cell Analysis
tensorflow instance-segmentation cell-biology deep-learning
Python
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Other
•99•423•47•1•Updated Aug 30, 2024Aug 30, 2024
Caliban-2024_Schwartz_et_al
Public
Jupyter Notebook
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Apache License 2.0
•0•2•0•0•Updated Aug 8, 2024Aug 8, 2024
deepcell-tracking
Public
Track cells and build cell lineages
Python
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Other
•6•27•8•0•Updated Aug 6, 2024Aug 6, 2024
cellSAM
Public
Codebase for "A Foundation Model for Cell Segmentation"
Jupyter Notebook
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Other
•8•53•14•3•Updated Aug 2, 2024Aug 2, 2024
deepcell-spots
Public
Deep Learning Library for Spot Detection
biological-data-analysis spot-detection deep-learning tensorflow
Python
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Other
•4•14•1•0•Updated Mar 15, 2024Mar 15, 2024
deepcell-label
Public
Cloud-based data annotation tools for biological images
react javascript python flask biology image-segmentation annotate-images xstate
JavaScript
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Other
•14•76•61•8•Updated Feb 14, 2024Feb 14, 2024
Polaris-2023_Laubscher_et_al
Public
Jupyter Notebook
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Other
•1•0•0•0•Updated Jan 31, 2024Jan 31, 2024
hubmap-mean-expression-example
Public
Minimal analysis example of data from cytokit+sprm pipeline output
Python
•0•0•0•0•Updated Dec 19, 2023Dec 19, 2023
deepcell-toolbox
Public
Data processing tools associated with deepcell
Python
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Other
•10•10•7•0•Updated Nov 7, 2023Nov 7, 2023
deepcelltypes-demo-08-2023
Public
Executable demo of deepcelltypes model pipeline
Python
•0•0•0•0•Updated Aug 26, 2023Aug 26, 2023
kiosk-imageJ-plugin
Public
An ImageJ Plugin for interacting with the DeepCell Kiosk
Java
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Other
•2•3•9•2•Updated Aug 24, 2023Aug 24, 2023
kiosk-console
Public
DeepCell Kiosk Distribution for Kubernetes on GKE and AWS
helm tensorflow-serving helmfile kubernetes
Shell
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Other
•6•35•15•0•Updated Jul 12, 2023Jul 12, 2023
kiosk-redis-consumer
Public
Consume the Kiosk's Redis Events
Python
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Other
•0•0•6•1•Updated Jul 12, 2023Jul 12, 2023
deepcell-label-processing
Public
Scripts for processing and converting raw data to label format and creating DCL projects
Python
•1•1•0•1•Updated Jul 7, 2023Jul 7, 2023
kiosk-data-processing
Public
DEPRECATED: gRPC API for pre- and post-processing data
Python
•0•0•0•2•Updated Jul 5, 2023Jul 5, 2023
deepcell-datasets
Public
React App for hosting curated datasets.
react serverless
Python
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Other
•0•0•11•7•Updated Jun 26, 2023Jun 26, 2023
bebi205
Public
Repo for Caltech's Be/Bi 205 course
Jupyter Notebook
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Other
•0•0•0•0•Updated May 31, 2023May 31, 2023
deepcell-applications
Public
Run DeepCell Applications
docker deep-learning image-processing instance-segmentation
Python
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Other
•6•8•3•0•Updated Apr 19, 2023Apr 19, 2023
kiosk-frontend
Public
DeepCell web application built using NodeJS, Express, React, and Webpack.
JavaScript
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Other
•0•1•6•8•Updated Feb 3, 2023Feb 3, 2023
deepcell-label-utils
Public
Utilities for spatial cell labels
Python
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Other
•0•0•0•0•Updated Sep 29, 2022Sep 29, 2022
kiosk-redis-janitor
Public
Watches Redis and restarts any stalled jobs.
Python
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Other
•0•0•1•0•Updated Jun 30, 2022Jun 30, 2022
kiosk-autoscaler
Public
Automatically and efficiently scale Kubernetes GPU resources
Python
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Other
•0•1•1•0•Updated Jun 30, 2022Jun 30, 2022
kiosk-tf-serving
Public
TensorFlow Serving with models hosted in the cloud
Python
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Other
•0•0•2•0•Updated Jun 1, 2022Jun 1, 2022
publication-figures
Public
Scripts capable of re-creating figures from Van Valen Lab publications
Jupyter Notebook
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Other
•3•18•1•0•Updated May 9, 2022May 9, 2022
tensorflow-serving-dockerfiles
Public
Apache License 2.0
•0•0•0•0•Updated May 5, 2022May 5, 2022
kiosk-client
Public
HTTP client utilities for interacting with the Deepcell kiosk
Python
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Other
•0•2•2•0•Updated Feb 16, 2022Feb 16, 2022
kiosk-bucket-monitor
Public
Monitors a cloud bucket and remove stale files.
Python
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Other
•0•0•1•0•Updated Dec 15, 2021Dec 15, 2021
tcga-utils
Public
Utilities for handling whole slide images from the The Cancer Genome Atlas (TCGA) Dataset
Python
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Other
•2•6•0•2•Updated Dec 14, 2021Dec 14, 2021
deepcell-retinamask
Public
RetinaNet and RetinaMask models for object detection based on TensorFlow and DeepCell-tf.
object-detection maskrcnn retinanet tensorflow
Python
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Other
•0•1•2•0•Updated Nov 29, 2021Nov 29, 2021