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Allen Institute for Cell Sciences

Username    aicspypi
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44 projects

aicspylibczi

Last released

A python module and a python extension for Zeiss (CZI/ZISRAW) microscopy files.

cyto-dl

Last released

Collection of representation learning models, techniques, callbacks, utils, used to create latent variable models of cell shape, morphology and intracellular organization.

bioio-ome-zarr

Last released

A BioIO reader plugin for reading Zarr files in the OME format.

bioio

Last released

Image reading, metadata management, and image writing for Microscopy images in Python

bioio-base

Last released

Typing, base classes, and more for BioIO projects.

simulariumio

Last released

Python package that converts simulation outputs to the format consumed by the Simularium viewer website

agave-pyclient

Last released

A Python client for the Agave 3d volume renderer

aicscytoparam

Last released

Cytoplasm parameterization using spherical harmonics

aicsshparam

Last released

Spherical harmonics parametrization for 3D starlike shapes

cvapipe-analysis

Last released

Analysis pipeline usinf in Integrated intracellular organization and its variations in human iPS cells

bioio-sldy

Last released

A BioIO reader plugin for reading 3i slidebook (SLDY) images.

bioio-nd2

Last released

A BioIO reader plugin for reading ND2 images.

bioio-tifffile

Last released

A BioIO reader plugin for reading TIFFs using Tifffile

bioio-tiff-glob

Last released

A BioIo reader for reading Tiff Glob images

bioio-ome-tiled-tiff

Last released

A BioIO reader plugin for reading tiled ome.tiff images.

bioio-bioformats

Last released

A BioIO reader for reading bioformats formatted images.

bioio-imageio

Last released

A BioIO reader plugin for reading simple image formats using imageio.

bioio-lif

Last released

A BioIO reader plugin for reading LIF (Leica Image File) images.

bioio-dv

Last released

A BioIO reader plugin for reading Digital Video (DV) files.

bioio-ome-tiff

Last released

A BioIO reader plugin for reading tiff files in the OME format.

bioio-czi

Last released

A Bioio reader plugin for reading czi images.

aicsimageio

Last released

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

aics-dask-utils

Last released

Utility functions and documentation related to Dask and AICS

napari-allencell-segmenter

Last released

A plugin that enables 3D image segmentation provided by Allen Institute for Cell Science

aicssegmentation

Last released

Part 1 of Allen Cell and Structure Segmenter

nbvv

Last released

Interactive volumetric voxel viewing

aicsimageprocessing

Last released

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

serotiny

Last released

A framework of tools to structure, configure and drive deep learning projects

simularium-metrics-calculator

Last released

Calculate plot metrics from spatial agent data

bioio-types

Last released

Typing, base classes, and more for BioIO projects.

napari-aicsimageio

Last released

AICSImageIO bindings for napari

segmenter-model-zoo

Last released

scripts and API for running Deep Learning models from segmenter

quilt3distribute

Last released

A small wrapper around quilt3 to make distributing manifest style datasets even easier.

microscope-automation

Last released

Automation software for the AICS Microscopes.

actk

Last released

Automated Cell Toolkit

aics-tf-registration

Last released

Rigid registration algorithm for generating training/testing data for transfer function model

datastep

Last released

A base class and utilities for creating steps in DAGs that are tied to large amounts of data.

aicsmlsegment

Last released

Scripts for ML structure segmentation.

image-classifier-3d

Last released

Python package for building 3d image classifier using deep neural networks

scheduler-tools

Last released

Tools for composing interdependent tasks on a scheduler (i.e. SLURM)

aicsdaemon

Last released

Python Class defining a daemon process. An implemented class that inherts from this should be runnable as a daemon.

oldaicsimageio

Last released

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

aicsfeature

Last released

Scripts for image features calculation.

qcb-plotting-tools

Last released

Plotting and Analysis tools for QCB

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