47 projects
cyto-dl
Collection of representation learning models, techniques, callbacks, utils, used to create latent variable models of cell shape, morphology and intracellular organization.
allencell-segmenter-ml
A plugin to leverage ML segmentation in napari
bioio-ome-tiff
A BioIO reader plugin for reading tiff files in the OME format.
cell-feature-data
A Python package for creating a dataset for the Cell Feature Explorer.
agave-pyclient
A Python client for the Agave 3d volume renderer
bioio-sldy
A BioIO reader plugin for reading 3i slidebook (SLDY) images.
napari-allencell-annotator
A plugin that enables annotations provided by Allen Institute for Cell Science
bioio
Image reading, metadata management, and image writing for Microscopy images in Python
bioio-ome-zarr
A BioIO reader plugin for reading Zarr files in the OME format.
bioio-czi
A Bioio reader plugin for reading czi images.
bioio-base
Typing, base classes, and more for BioIO projects.
aicspylibczi
A python module and a python extension for Zeiss (CZI/ZISRAW) microscopy files.
simulariumio
Python package that converts simulation outputs to the format consumed by the Simularium viewer website
aicscytoparam
Cytoplasm parameterization using spherical harmonics
aicsshparam
Spherical harmonics parametrization for 3D starlike shapes
cvapipe-analysis
Analysis pipeline usinf in Integrated intracellular organization and its variations in human iPS cells
bioio-nd2
A BioIO reader plugin for reading ND2 images.
bioio-tifffile
A BioIO reader plugin for reading TIFFs using Tifffile
bioio-tiff-glob
A BioIo reader for reading Tiff Glob images
bioio-ome-tiled-tiff
A BioIO reader plugin for reading tiled ome.tiff images.
bioio-bioformats
A BioIO reader for reading bioformats formatted images.
bioio-imageio
A BioIO reader plugin for reading simple image formats using imageio.
bioio-lif
A BioIO reader plugin for reading LIF (Leica Image File) images.
bioio-dv
A BioIO reader plugin for reading Digital Video (DV) files.
aicsimageio
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python
aics-dask-utils
Utility functions and documentation related to Dask and AICS
napari-allencell-segmenter
A plugin that enables 3D image segmentation provided by Allen Institute for Cell Science
aicssegmentation
Part 1 of Allen Cell and Structure Segmenter
nbvv
Interactive volumetric voxel viewing
aicsimageprocessing
A generalized scientific image processing module from the Allen Institute for Cell Science.
serotiny
A framework of tools to structure, configure and drive deep learning projects
simularium-metrics-calculator
Calculate plot metrics from spatial agent data
bioio-types
Typing, base classes, and more for BioIO projects.
napari-aicsimageio
AICSImageIO bindings for napari
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
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
