Projects in Awesome Lists by AllenCellModeling
A curated list of projects in awesome lists by AllenCellModeling .
https://github.com/AllenCellModeling/aicsimageio
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
bio-formats dask image-metadata imageio microscopy python scientific-computing scientific-formats xarray
Last synced: 07 May 2025
https://github.com/allencellmodeling/aicsimageio
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
bio-formats dask image-metadata imageio microscopy python scientific-computing scientific-formats xarray
Last synced: 14 Apr 2025
https://github.com/allencellmodeling/pytorch_fnet
Three dimensional cross-modal image inference
Last synced: 20 Dec 2024
https://github.com/allencellmodeling/torch_integrated_cell
biolog cell-analysis machine-learning neural-network torch
Last synced: 30 Apr 2025
https://github.com/allencellmodeling/pytorch_integrated_cell
Integrated Cell project implemented in pytorch
autoencoder cell-analysis cell-biology generative-adversarial-network machine-learning neural-networks python pytorch science-research
Last synced: 30 Apr 2025
https://github.com/AllenCellModeling/napari-aicsimageio
Multiple file format reading directly into napari using pure Python
Last synced: 07 May 2025
https://github.com/allencellmodeling/napari-aicsimageio
Multiple file format reading directly into napari using pure Python
Last synced: 14 Apr 2025
https://github.com/allencellmodeling/nvidia-docker-stats
Monitor nvidia gpu unit load associated with docker spawned processes
Last synced: 30 Apr 2025
https://github.com/allencellmodeling/actk
Automated Cell Toolkit
biology cell-biology image-processing microscopy pipeline
Last synced: 30 Apr 2025
https://github.com/allencellmodeling/cookiecutter-pypackage
A cookiecutter template to generate a new Python package.
Last synced: 30 Apr 2025
https://github.com/allencellmodeling/czifile
czi reader from https://www.lfd.uci.edu/~gohlke/code/czifile.py.html
Last synced: 30 Apr 2025
https://github.com/allencellmodeling/allencellmodeling.github.io
Data stories
Last synced: 30 Apr 2025
https://github.com/allencellmodeling/dlite
Let's infer the forces that cells generate during time series by looking at the angles they make with each other.
Last synced: 30 Apr 2025
https://github.com/allencellmodeling/quilt3distribute
People commonly work with tabular datasets, people want to share their data, this makes that easier through Quilt3.
Last synced: 30 Apr 2025
https://github.com/allencellmodeling/fish_morphology_code
Basic code and automated workflows to produce analysis friendly data from annotated FISH images
Last synced: 30 Apr 2025
https://github.com/allencellmodeling/quiltloader
Adding custom attributes to quilt nodes
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/diffusive_distinguishability
Simulation of homogeneous diffusion, bayesian estimation of underlying diffusion constant, and analysis of distinguishability between diffusivity estimates
bayesian-inference diffusion single-particle-motion trajectory-analysis
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/cvae_testbed
A research testbed on conditional variational autoencoders using Gaussian distributions as input
Last synced: 30 Apr 2025
https://github.com/allencellmodeling/czi-to-ome-xslt
A repository of XSL transform sheets to map CZI metadata to OME.
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/datastep
A base class and utility functions for creating pure functions steps for DAGs.
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/cookiecutter-stepworkflow
AICS Cookiecutter Template for a simple data + code workflow
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/long-term-eng
Long Term Engineering + Infrastructure Projects
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/elastic_net_gene_selection
scRNA-seq gene selection code
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/aics-deformation
Tools to use when working on deformation projects.
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/bioloaders
A repository of dataset objects for common datatypes in bio sciences.
Last synced: 30 Apr 2025
https://github.com/allencellmodeling/aics_dask_utils
Utility functions commonly used by AICS projects for interacting with Dask
Last synced: 22 Feb 2025
https://github.com/AllenCellModeling/cookiecutter-stepworkflow
AICS Cookiecutter Template for a simple data + code workflow
Last synced: 08 May 2025
https://github.com/allencellmodeling/fish_morphology_manuscript_notebooks
Notebooks for figures in our manuscript
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/flins
Simulate a system of linear filaments
biophysics cell-biology muscle stress-fibers
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/jupyter_notebook_conda_server
Scripts to set up a Jupiter notebook server that allows you to access your other Conda environments as Jupyter notebook kernels
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/polar_express
Distributed DataStep pipeline to process 3D microscopy images, perform large-scale statistical analysis, and generate summary visualizations for the data.
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/py_saxon_c
This is a copy of Saxonicas C & Python libraries so I can tidy up the install a bit and make it a package dependency without hand building it.
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/c6
Circular center-based cell colony creation and clustering
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/mitoclassifier
This is an implementation of an image based classifier that can be trained to distinguish cell cycle events.
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/aicsimageio-ometiffreader
ome tiff reader for aicsimageio
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/pytorch_learning_tools
classification and regression tools for pytorch
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/lineannotation
GUI tool for creating training data to determine sarcomere length
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/dbormexample
Using Orator to populate a DB
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/colabnotebookexamples
Colab Notebooks with example deep learning experiments using AICS data
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/workflow_colony_formation
Model of colony formation informed by timelapse video of replated cells.
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/example_step_workflow
An example step workflow that does a whole bunch of simple random matrix inversion.
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/crossmodal
Cross modal analysis of RNA seq and images
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/lightgbm_mito
mitotic classification using features data and gradient boosted decision trees
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/r_cardiodiff_rnaseq_analysis
R notebooks and docker file for rna-seq data analysis
Last synced: 22 Feb 2025
https://github.com/allencellmodeling/aicsdaemon
This is a daemon class to inherit from in order to transform python commands into a linux daemon
Last synced: 22 Feb 2025