vanvalenlab/deepcell-spots

Deep Learning Library for Spot Detection

Language: Python - Size: 211 MB - Last synced: 11 days ago - Pushed: 2 months ago - Stars: 11 - Forks: 2

vanvalenlab/bebi205

Repo for Caltech's Be/Bi 205 course

Language: Jupyter Notebook - Size: 26.2 MB - Last synced: 28 days ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

vanvalenlab/deepcell-tf

Deep Learning Library for Single Cell Analysis

Language: Python - Size: 340 MB - Last synced: 20 days ago - Pushed: about 2 months ago - Stars: 391 - Forks: 90

vanvalenlab/cellSAM

Codebase for "A Foundation Model for Cell Segmentation"

Language: Jupyter Notebook - Size: 1.47 MB - Last synced: 16 days ago - Pushed: about 2 months ago - Stars: 9 - Forks: 3

vanvalenlab/deepcell-tracking

Track cells and build cell lineages

Language: Python - Size: 359 KB - Last synced: 29 days ago - Pushed: about 1 year ago - Stars: 23 - Forks: 7

vanvalenlab/deepcell-label

Cloud-based data annotation tools for biological images

Language: JavaScript - Size: 41.8 MB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 67 - Forks: 14

vanvalenlab/hubmap-mean-expression-example

Minimal analysis example of data from cytokit+sprm pipeline output

Language: Python - Size: 2.93 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

vanvalenlab/intro-to-deepcell

An introduction to deepcell and deep learning

Language: Jupyter Notebook - Size: 23.9 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 121 - Forks: 24

vanvalenlab/deepcell-toolbox

Data processing tools associated with deepcell

Language: Python - Size: 439 KB - Last synced: 28 days ago - Pushed: 7 months ago - Stars: 8 - Forks: 9

vanvalenlab/Polaris-2023_Laubscher_et_al

Language: Jupyter Notebook - Size: 245 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

vanvalenlab/Caliban-2023_Schwartz_et_al

Language: Jupyter Notebook - Size: 2.15 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

vanvalenlab/deepcelltypes-demo-08-2023

Executable demo of deepcelltypes model pipeline

Language: Python - Size: 15.6 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

vanvalenlab/caliban-toolbox

Data engineering toolbox for DeepCell

Language: Jupyter Notebook - Size: 152 MB - Last synced: 7 days ago - Pushed: almost 3 years ago - Stars: 7 - Forks: 1

vanvalenlab/deepcell-label-processing

Scripts for processing and converting raw data to label format and creating DCL projects

Language: Python - Size: 55.7 KB - Last synced: 8 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 1

vanvalenlab/kiosk-console

DeepCell Kiosk Distribution for Kubernetes on GKE and AWS

Language: Shell - Size: 18.7 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 32 - Forks: 5

vanvalenlab/publication-figures

Scripts capable of re-creating figures from Van Valen Lab publications

Language: Jupyter Notebook - Size: 15.1 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 13 - Forks: 3

vanvalenlab/kiosk-tensorboard 📦

DEPRECATED: Monitor training progress with TensorBoard

Language: Dockerfile - Size: 9.77 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

vanvalenlab/kiosk-training 📦

DEPRECATED: Training files for kiosk

Language: Python - Size: 36.1 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

vanvalenlab/deepcell-applications

Run DeepCell Applications

Language: Python - Size: 43.9 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 4 - Forks: 5

vanvalenlab/kiosk-imageJ-plugin

An ImageJ Plugin for interacting with the DeepCell Kiosk

Language: Java - Size: 1.11 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 2 - Forks: 2

vanvalenlab/deepcell-retinamask

RetinaNet and RetinaMask models for object detection based on TensorFlow and DeepCell-tf.

Language: Python - Size: 2.05 MB - Last synced: 30 days ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

vanvalenlab/deepcell-label-utils

Utilities for spatial cell labels

Language: Python - Size: 19.5 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

vanvalenlab/tensorflow-serving-dockerfiles

Size: 8.79 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

vanvalenlab/tcga-utils

Utilities for handling whole slide images from the The Cancer Genome Atlas (TCGA) Dataset

Language: Python - Size: 20.2 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 5 - Forks: 2

vanvalenlab/kiosk-frontend

DeepCell web application built using NodeJS, Express, React, and Webpack.

Language: JavaScript - Size: 6.65 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

vanvalenlab/kiosk-autoscaler

Automatically and efficiently scale Kubernetes GPU resources

Language: Python - Size: 105 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

vanvalenlab/kiosk-redis-janitor

Watches Redis and restarts any stalled jobs.

Language: Python - Size: 87.9 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

vanvalenlab/deepcell-datasets

React App for hosting curated datasets.

Language: Python - Size: 16.1 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

vanvalenlab/kiosk-redis-consumer

Consume the Kiosk's Redis Events

Language: Python - Size: 519 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

vanvalenlab/kiosk-bucket-monitor

Monitors a cloud bucket and remove stale files.

Language: Python - Size: 56.6 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

vanvalenlab/kiosk-client

HTTP client utilities for interacting with the Deepcell kiosk

Language: Python - Size: 197 KB - Last synced: 22 days ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

vanvalenlab/kiosk-tf-serving

TensorFlow Serving with models hosted in the cloud

Language: Python - Size: 46.2 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

vanvalenlab/cloud-notebook-runner

Runs parameterized Jupyter notebooks with papermill on google cloud compute instances

Language: Python - Size: 7.81 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 1

vanvalenlab/kiosk-data-processing

DEPRECATED: gRPC API for pre- and post-processing data

Language: Python - Size: 54.7 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0