Allen Institute for Cell Science - Modeling 's repositories
aicsimageio
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
pytorch_integrated_cell
Integrated Cell project implemented in pytorch
aicspylibczi
Python module utilizing libCZI for reading Zeiss CZI files.
napari-aicsimageio
Multiple file format reading directly into napari using pure Python
nvidia-docker-stats
Monitor nvidia gpu unit load associated with docker spawned processes
cookiecutter-pypackage
A cookiecutter template to generate a new Python package.
quilt3distribute
People commonly work with tabular datasets, people want to share their data, this makes that easier through Quilt3.
CVAE_testbed
A research testbed on conditional variational autoencoders using Gaussian distributions as input
fish_morphology_code
Basic code and automated workflows to produce analysis friendly data from annotated FISH images
aicsimageprocessing
A generalized scientific image processing module from the Allen Institute for Cell Science.
czi-to-ome-xslt
A repository of XSL transform sheets to map CZI metadata to OME.
aics_dask_utils
Utility functions commonly used by AICS projects for interacting with Dask
bioloaders
A repository of dataset objects for common datatypes in bio sciences.
cell-tracker-gnn
[ECCV 2022] Official PyTorch implementation of the paper - Graph Neural Network for Cell Tracking in Microscopy Videos
cookiecutter-stepworkflow
AICS Cookiecutter Template for a simple data + code workflow
fish_morphology_manuscript_notebooks
Notebooks for figures in our manuscript
aicsimageio-ometiffreader
ome tiff reader for aicsimageio
ColabNotebookExamples
Colab Notebooks with example deep learning experiments using AICS data
crossmodal
Cross modal analysis of RNA seq and images
serotiny-project-cookiecutter
a cookiecutter to set up serotiny templates
timelapse_tools
Load and convert 🎥