Allen Institute for Cell Science - Modeling

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76 repositories

czifile
Public archive
czi reader from https://www.lfd.uci.edu/~gohlke/code/czifile.py.html
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•6•15•3•1•Updated Oct 15, 2025Oct 15, 2025
pytorch_fnet
Public archive
Three dimensional cross-modal image inference
Python
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Other
•67•160•34•1•Updated Oct 15, 2025Oct 15, 2025
CVAE_testbed
Public archive
A research testbed on conditional variational autoencoders using Gaussian distributions as input
Jupyter Notebook
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Other
•2•3•0•2•Updated Oct 15, 2025Oct 15, 2025
brightfield2fish
Public archive
Python
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Other
•0•2•5•0•Updated Oct 15, 2025Oct 15, 2025
DLITE
Public archive
Let's infer the forces that cells generate during time series by looking at the angles they make with each other.
Jupyter Notebook
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Other
•3•9•1•3•Updated Oct 15, 2025Oct 15, 2025
diffusive_distinguishability
Public archive
Simulation of homogeneous diffusion, bayesian estimation of underlying diffusion constant, and analysis of distinguishability between diffusivity estimates
bayesian-inference trajectory-analysis diffusion single-particle-motion
Jupyter Notebook
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Other
•1•3•0•0•Updated Oct 15, 2025Oct 15, 2025
seq2loc
Public archive
Jupyter Notebook
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GNU General Public License v3.0
•0•3•4•0•Updated Oct 15, 2025Oct 15, 2025
fish_morphology_code
Public archive
Basic code and automated workflows to produce analysis friendly data from annotated FISH images
Python
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Other
•2•4•5•4•Updated Oct 15, 2025Oct 15, 2025
QuiltLoader
Public archive
Adding custom attributes to quilt nodes
Python
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GNU General Public License v3.0
•0•4•0•0•Updated Oct 15, 2025Oct 15, 2025
napari-annotation-tools
Public archive
Python
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Other
•0•5•3•0•Updated Oct 15, 2025Oct 15, 2025
long-term-eng
Public archive
Long Term Engineering + Infrastructure Projects
0•1•4•0•Updated Oct 15, 2025Oct 15, 2025
fish_morphology_manuscript_notebooks
Public archive
Notebooks for figures in our manuscript
Jupyter Notebook
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Other
•0•1•0•0•Updated Oct 15, 2025Oct 15, 2025
AllenCellModeling.github.io
Public archive
Data stories
Jupyter Notebook
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MIT License
•6•10•4•0•Updated Oct 15, 2025Oct 15, 2025
datastep
Public archive
A base class and utility functions for creating pure functions steps for DAGs.
Python
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Other
•0•1•6•0•Updated Oct 15, 2025Oct 15, 2025
actk
Public archive
Automated Cell Toolkit
pipeline biology image-processing microscopy cell-biology
Python
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Other
•4•24•3•1•Updated Oct 15, 2025Oct 15, 2025
napari-aicsimageio
Public
Multiple file format reading directly into napari using pure Python
imageio microscopy napari
Python
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GNU General Public License v3.0
•13•38•17•3•Updated Oct 15, 2025Oct 15, 2025
cookiecutter-stepworkflow
Public archive
AICS Cookiecutter Template for a simple data + code workflow
Python
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MIT License
•0•1•0•0•Updated Oct 15, 2025Oct 15, 2025
pytorch_integrated_cell
Public archive
Integrated Cell project implemented in pytorch
python machine-learning pytorch generative-adversarial-network neural-networks autoencoder science-research cell-analysis cell-biology
Python
•13•44•27•4•Updated Oct 15, 2025Oct 15, 2025
bioloaders
Public archive
A repository of dataset objects for common datatypes in bio sciences.
Python
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Other
•3•1•0•2•Updated Oct 15, 2025Oct 15, 2025
aics-deformation
Public archive
Tools to use when working on deformation projects.
Python
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Other
•0•1•0•0•Updated Oct 15, 2025Oct 15, 2025
torch_integrated_cell
Public archive
machine-learning neural-network torch cell-analysis biolog
Jupyter Notebook
•8•46•0•0•Updated Oct 15, 2025Oct 15, 2025
cyto-dl
Public
Python
•8•27•10•5•Updated Sep 26, 2025Sep 26, 2025
aicspylibczi
Public
Python module utilizing libCZI for reading Zeiss CZI files.
C++
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GNU General Public License v3.0
•10•42•15•0•Updated Apr 14, 2025Apr 14, 2025
fov_processing_pipeline
Public archive
Python
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Other
•0•0•8•1•Updated Mar 26, 2025Mar 26, 2025
aicsimageio
Public
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
python xarray scientific-computing imageio bio-formats dask image-metadata microscopy scientific-formats
Python
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Other
•51•220•2•0•Updated Jan 15, 2025Jan 15, 2025
czi-to-ome-xslt
Public
A repository of XSL transform sheets to map CZI metadata to OME.
XSLT
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Other
•0•2•6•0•Updated Dec 13, 2024Dec 13, 2024
pointcloudutils
Public
Python
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Other
•0•0•0•0•Updated Apr 17, 2024Apr 17, 2024
nvidia-docker-stats
Public
Monitor nvidia gpu unit load associated with docker spawned processes
Python
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GNU General Public License v3.0
•13•29•1•2•Updated Oct 1, 2023Oct 1, 2023
aics_dask_utils
Public
Utility functions commonly used by AICS projects for interacting with Dask
Python
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Other
•0•1•2•0•Updated Aug 10, 2023Aug 10, 2023
aicsimageprocessing
Public archive
A generalized scientific image processing module from the Allen Institute for Cell Science.
Python
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Other
•1•2•1•1•Updated Aug 2, 2023Aug 2, 2023