Allen Institute for Cell Science

Allen Institute Open Source projects for general use.

Seattle, WA

Pinned Repositories

aics-cytoparam
Language:Python7 7 21
aics-ml-segmentation
Language:Python30 6 77
aics-segmentation
Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow
Language:Jupyter Notebook27 9 2212
aics-shparam
Language:Python20 8 24
cvapipe_analysis
Analysis of data produced by cvapipe for the variance paper
Language:Jupyter Notebook22 7 196
napari-allencell-segmenter
A plugin that enables image segmentation provided by Allen Institute for Cell Science
Language:Python16 11 1056
quilt-data-access-tutorials
A collection of tutorials for accessing allen cell quilt packages
Language:Jupyter Notebook52
segmenter_model_zoo
scripts and API for running Deep Learning models from segmenter
Language:Jupyter Notebook10 9 21
serotiny
Tools for pytorch machine learning pipelines
Language:Python8 4 461
stemcellorganellesizescaling
Language:Python5 8 01

Allen Institute for Cell Science's Repositories

AllenCell/aics-ml-segmentation
Language:Python30 6 77
AllenCell/aics-segmentation
Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow
Language:Jupyter Notebook27 9 2212
AllenCell/cvapipe_analysis
Analysis of data produced by cvapipe for the variance paper
Language:Jupyter Notebook22 7 196
AllenCell/aics-shparam
Language:Python20 8 24
AllenCell/napari-allencell-segmenter
A plugin that enables image segmentation provided by Allen Institute for Cell Science
Language:Python16 11 1056
AllenCell/segmenter_model_zoo
scripts and API for running Deep Learning models from segmenter
Language:Jupyter Notebook10 9 21
AllenCell/serotiny
Tools for pytorch machine learning pipelines
Language:Python8 4 461
AllenCell/aics-cytoparam
Language:Python7 7 21
AllenCell/quilt-data-access-tutorials
A collection of tutorials for accessing allen cell quilt packages
Language:Jupyter Notebook52
AllenCell/stemcellorganellesizescaling
Language:Python5 8 01
AllenCell/cvapipe_figure_notebooks
Notebooks for reproducing figures in the cell variance paper
Language:Jupyter Notebook4 4 00
AllenCell/cytodata-3d-shape-analysis
Language:Jupyter Notebook4 5 01
AllenCell/PairUPWorkshop
Codebase for the PairUP Workshop held at Allen Institute for Cell Science
Language:Jupyter Notebook33
AllenCell/aicsfeature
a central code base for cell feature calculate in different applications
Language:Python2 5 00
AllenCell/allencell-segmenter-ml
Napari plugin for ml segmentation
Language:Python21
AllenCell/benchmarking_representations
Benchmarking different methods for extracting unsupervised representations from images
Language:Python21
AllenCell/colony-processing
code for 12X colony image processing, dataset creatation and analysis
Language:Jupyter Notebook2
AllenCell/cvapipe
Cell Variance Analysis Pipeline
Language:Python2
AllenCell/image_classifier_3d
Python package for 3D image classification using deep neural network
Language:Python2
AllenCell/cardio_scrnaseq_paper_code
Language:Jupyter Notebook1 4 1
AllenCell/cytodata-hackathon-base
Language:Jupyter Notebook1 8 27
AllenCell/EMT_data_analysis
This repo contains code for EMT deliverable data analysis and has dependencies associated with output from EMT_image_analysis repo.
Language:Python1
AllenCell/EMT_image_analysis
Repository for EMT image analysis code
Language:Python10
AllenCell/morflowgenesis
Language:Python00
AllenCell/aics-timelapse-tracking
Language:Python
AllenCell/aics-track-curator
Language:Python
AllenCell/camera-alignment-core
Core algorithms for alignment of two-camera microscopy imagery
Language:Python1
AllenCell/i2k_workshop_2024
CytoDL demo for I2K 2024
Language:Jupyter Notebook
AllenCell/nuc-morph-analysis
Language:Python
AllenCell/open-data-registry
A registry of publicly available datasets on AWS
Language:Python