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actk

Automated Cell Toolkit

aics-deformation

Tools to use when working on deformation projects.

aics-fms-file-explorer-app

AICS FMS File Explorer Front End

aics_dask_utils

Utility functions commonly used by AICS projects for interacting with Dask

aicsdaemon

This is a daemon class to inherit from in order to transform python commands into a linux daemon

aicsimage

Image IO for CZI, OME-TIFF, and PNGs

aicsimageio

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

aicsimageio-ometiffreader

ome tiff reader for aicsimageio

aicsimageprocessing

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

aicspylibczi

Python module utilizing libCZI for reading Zeiss CZI files.

allencellmodeling.github.io

Data stories

bioloaders

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

brightfield2fish

c6

Circular center-based cell colony creation and clustering

cell-tracker-gnn

[ECCV 2022] Official PyTorch implementation of the paper - Graph Neural Network for Cell Tracking in Microscopy Videos

colabnotebookexamples

Colab Notebooks with example deep learning experiments using AICS data

cookiecutter-pypackage

A cookiecutter template to generate a new Python package.

cookiecutter-stepworkflow

AICS Cookiecutter Template for a simple data + code workflow

crossmodal

Cross modal analysis of RNA seq and images

cvae_testbed

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

cyto-dl

czi-to-ome-xslt

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

czifile

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

datasetdatabase

Modeling DB Schema, Creation, and IO

datastep

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

dbormexample

Using Orator to populate a DB

diffusive_distinguishability

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

dlite

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

docker_anaconda3_extended

Docker image that extends the anaconda3 image with some Jupyter conveniences.

docker_pytorch_extended

Uses the pytorch docker image to build an extended image with jupyter notebook, and some other python utils