28 projects
nbvv
Interactive volumetric voxel viewing
simulariumio
Python package that converts simulation outputs to the format consumed by the Simularium viewer website
aicsimageio
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python
agave-pyclient
A Python client for the Agave 3d volume renderer
aicscytoparam
Cytoplasm parameterization using spherical harmonics
aicsshparam
Spherical harmonics parametrization for 3D starlike shapes
aicspylibczi
A python module and a python extension for Zeiss (CZI/ZISRAW) microscopy files.
aicsimageprocessing
A generalized scientific image processing module from the Allen Institute for Cell Science.
napari-allencell-segmenter
A plugin that enables 3D image segmentation provided by Allen Institute for Cell Science
serotiny
A framework of tools to structure, configure and drive deep learning projects
cvapipe-analysis
Analysis of data produced by cvapipe for the variance paper
simularium-metrics-calculator
Calculate plot metrics from spatial agent data
napari-aicsimageio
AICSImageIO bindings for napari
aicssegmentation
Part 1 of Allen Cell and Structure Segmenter
segmenter-model-zoo
scripts and API for running Deep Learning models from segmenter
quilt3distribute
A small wrapper around quilt3 to make distributing manifest style datasets even easier.
microscope-automation
Automation software for the AICS Microscopes.
actk
Automated Cell Toolkit
aics-tf-registration
Rigid registration algorithm for generating training/testing data for transfer function model
datastep
A base class and utilities for creating steps in DAGs that are tied to large amounts of data.
aicsmlsegment
Scripts for ML structure segmentation.
image-classifier-3d
Python package for building 3d image classifier using deep neural networks
aics-dask-utils
Utility functions and documentation related to Dask and AICS
scheduler-tools
Tools for composing interdependent tasks on a scheduler (i.e. SLURM)
aicsdaemon
Python Class defining a daemon process. An implemented class that inherts from this should be runnable as a daemon.
oldaicsimageio
A generalized scientific image processing module from the Allen Institute for Cell Science.
aicsfeature
Scripts for image features calculation.
qcb-plotting-tools
Plotting and Analysis tools for QCB