Explore @AllenCellModeling Open Source projects

Allen Institute for Cell Science - Modeling (@AllenCellModeling)

AllenCellModeling

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584
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Registered over 7 years ago
Most used languages

Python
65.6 %

Jupyter Notebook
31.3 %

XSLT 3.1 %

aicsimageio

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

pytorch_fnet

Three dimensional cross-modal image inference

torch_integrated_cell

Jupyter Notebook

pytorch_integrated_cell

Integrated Cell project implemented in pytorch

napari-aicsimageio

Multiple file format reading directly into napari using pure Python

cookiecutter-pypackage

A cookiecutter template to generate a new Python package.

actk

Automated Cell Toolkit

nvidia-docker-stats

Monitor nvidia gpu unit load associated with docker spawned processes

czifile

czi reader from https://www.lfd.uci.edu/~gohlke/code/czifile.py.html

Jupyter Notebook

AllenCellModeling.github.io

Jupyter Notebook

DLITE

Let's infer the forces that cells generate during time series by looking at the angles they make with each other.

Jupyter Notebook

napari-annotation-tools

quilt3distribute

People commonly work with tabular datasets, people want to share their data, this makes that easier through Quilt3.

QuiltLoader

Adding custom attributes to quilt nodes

diffusive_distinguishability

Simulation of homogeneous diffusion, bayesian estimation of underlying diffusion constant, and analysis of distinguishability between diffusivity estimates

Jupyter Notebook

seq2loc

Jupyter Notebook

fish_morphology_code

Basic code and automated workflows to produce analysis friendly data from annotated FISH images

CVAE_testbed

A research testbed on conditional variational autoencoders using Gaussian distributions as input

Jupyter Notebook

aicsimage

Image IO for CZI, OME-TIFF, and PNGs

Jupyter Notebook

brightfield2fish

czi-to-ome-xslt

A repository of XSL transform sheets to map CZI metadata to OME.

aicsimageprocessing

A generalized scientific image processing module from the Allen Institute for Cell Science.

cookiecutter-stepworkflow

AICS Cookiecutter Template for a simple data + code workflow

aics_dask_utils

Utility functions commonly used by AICS projects for interacting with Dask

fish_morphology_manuscript_notebooks

Notebooks for figures in our manuscript

Jupyter Notebook

normal_mode_analysis

Normal mode analysis from meshes

Jupyter Notebook

long-term-eng

Long Term Engineering + Infrastructure Projects

aics-deformation

Tools to use when working on deformation projects.

datasetdatabase

Modeling DB Schema, Creation, and IO

elastic_net_gene_selection

scRNA-seq gene selection code

bioloaders

A repository of dataset objects for common datatypes in bio sciences.

datastep

A base class and utility functions for creating pure functions steps for DAGs.

cyto-dl