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aicsimageio
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pythonpytorch_fnet
Three dimensional cross-modal image inferencetorch_integrated_cell
pytorch_integrated_cell
Integrated Cell project implemented in pytorchnapari-aicsimageio
Multiple file format reading directly into napari using pure Pythoncookiecutter-pypackage
A cookiecutter template to generate a new Python package.actk
Automated Cell Toolkitnvidia-docker-stats
Monitor nvidia gpu unit load associated with docker spawned processesczifile
czi reader from https://www.lfd.uci.edu/~gohlke/code/czifile.py.htmlAllenCellModeling.github.io
Data storiesDLITE
Let's infer the forces that cells generate during time series by looking at the angles they make with each other.quilt3distribute
People commonly work with tabular datasets, people want to share their data, this makes that easier through Quilt3.QuiltLoader
Adding custom attributes to quilt nodesdiffusive_distinguishability
Simulation of homogeneous diffusion, bayesian estimation of underlying diffusion constant, and analysis of distinguishability between diffusivity estimatesseq2loc
fish_morphology_code
Basic code and automated workflows to produce analysis friendly data from annotated FISH imagesCVAE_testbed
A research testbed on conditional variational autoencoders using Gaussian distributions as inputaicsimage
Image IO for CZI, OME-TIFF, and PNGsbrightfield2fish
czi-to-ome-xslt
A repository of XSL transform sheets to map CZI metadata to OME.aicsimageprocessing
A generalized scientific image processing module from the Allen Institute for Cell Science.cookiecutter-stepworkflow
AICS Cookiecutter Template for a simple data + code workflowaics_dask_utils
Utility functions commonly used by AICS projects for interacting with Daskfish_morphology_manuscript_notebooks
Notebooks for figures in our manuscriptnormal_mode_analysis
Normal mode analysis from mesheslong-term-eng
Long Term Engineering + Infrastructure Projectsaics-deformation
Tools to use when working on deformation projects.datasetdatabase
Modeling DB Schema, Creation, and IOelastic_net_gene_selection
scRNA-seq gene selection codebioloaders
A repository of dataset objects for common datatypes in bio sciences.datastep
A base class and utility functions for creating pure functions steps for DAGs.cyto-dl
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