AllenCell/cytodata-hackathon-base

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AllenCell/cytodata-hackathon-base

AllenCell

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aics-ml-segmentation

aics-segmentation

Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow

Jupyter Notebook

cvapipe_analysis

Analysis of data produced by cvapipe for the variance paper

Jupyter Notebook

aics-shparam

napari-allencell-segmenter

A plugin that enables image segmentation provided by Allen Institute for Cell Science

segmenter_model_zoo

scripts and API for running Deep Learning models from segmenter

Jupyter Notebook

serotiny

Tools for pytorch machine learning pipelines

aics-cytoparam

quilt-data-access-tutorials

A collection of tutorials for accessing allen cell quilt packages

Jupyter Notebook

stemcellorganellesizescaling

cvapipe_figure_notebooks

Notebooks for reproducing figures in the cell variance paper

Jupyter Notebook

cytodata-3d-shape-analysis

Jupyter Notebook

PairUPWorkshop

Codebase for the PairUP Workshop held at Allen Institute for Cell Science

Jupyter Notebook

colony-processing

code for 12X colony image processing, dataset creatation and analysis

Jupyter Notebook

image_classifier_3d

Python package for 3D image classification using deep neural network

aicsfeature

a central code base for cell feature calculate in different applications

cvapipe

Cell Variance Analysis Pipeline

EMT_image_analysis

Repository for EMT image analysis code

cardio_scrnaseq_paper_code

Jupyter Notebook

allencell-segmenter-ml

Napari plugin for ml segmentation

EMT_data_analysis

This repo contains code for EMT deliverable data analysis and has dependencies associated with output from EMT_image_analysis repo.