48 projects
bioio-czi
A Bioio reader plugin for reading czi images.
bioio-nd2
A BioIO reader plugin for reading ND2 images.
bioio-bioformats
A BioIO reader for reading bioformats formatted images.
bioio
Image reading, metadata management, and image writing for Microscopy images in Python
bioio-base
Typing, base classes, and more for BioIO projects.
bioio-ome-zarr
A BioIO reader plugin for reading Zarr files in the OME format.
bioio-conversion
A BioIO conversion tool for going between image formats
agave-pyclient
A Python client for the Agave 3d volume renderer
bioio-sldy
A BioIO reader plugin for reading 3i slidebook (SLDY) images.
bioio-lif
A BioIO reader plugin for reading LIF (Leica Image File) images.
cyto-dl
Collection of representation learning models, techniques, callbacks, utils, used to create latent variable models of cell shape, morphology and intracellular organization.
napari-allencell-segmenter
A plugin that enables 3D image segmentation provided by Allen Institute for Cell Science
allencell-segmenter-ml
A plugin to leverage ML segmentation in napari
simulariumio
Python package that converts simulation outputs to the format consumed by the Simularium viewer website
bioio-ome-tiff
A BioIO reader plugin for reading tiff files in the OME format.
bioio-tifffile
A BioIO reader plugin for reading TIFFs using Tifffile
bioio-imageio
A BioIO reader plugin for reading simple image formats using imageio.
bioio-ome-tiled-tiff
A BioIO reader plugin for reading tiled ome.tiff images.
bioio-tiff-glob
A BioIo reader for reading Tiff Glob images
bioio-dv
A BioIO reader plugin for reading Digital Video (DV) files.
aicspylibczi
A python module and a python extension for Zeiss (CZI/ZISRAW) microscopy files.
aicscytoparam
Cytoplasm parameterization using spherical harmonics
aicsshparam
Spherical harmonics parametrization for 3D starlike shapes
cell-feature-data
A Python package for creating a dataset for the Cell Feature Explorer.
napari-allencell-annotator
A plugin that enables annotations provided by Allen Institute for Cell Science
cvapipe-analysis
Analysis pipeline usinf in Integrated intracellular organization and its variations in human iPS cells
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
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
