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croissant

Classifying regions of interest in mouse brain as cell or not cell

ctke_viz

Code used to generate data visualizations and text for the Cell Type Knowledge Explorer

dash_on_flask

Dash on Flask with login_required (and application factory pattern)

dashdataframe

An simplified interface for making dash apps to explore multi-dimensional dataframes with custom link integration and filtering.

data_ingest

The Allen Institute's data ingest system

datacube

deep-neurographs

Neuron reconstruction framework that detects and corrects false splits in a predicted segmentation.

deepcell

CNN-based classifier for classifying neuronal cell bodies from ROI segmentation masks

deepinterpolation

deepinterpolation_ai_internal

This repo is based on https://github.com/AllenInstitute/deepinterpolation however its primary function is for internal use only at the Allen Institute.

deepinterpolation_nextflow

deepinterpolation_paper

devrhesuslmd

Non-human primate brain development gene expression

dipde

Numerical solver for coupled population density equations

dispimdb

dlgn_cross_species

dmn

Supporting code for Whitesell et al., 2020 "Regional, layer, and cell-class specific connectivity of the mouse default mode network"

doc-pickle-tests

drcme

Dimensionality-reduction and classification for morphology and electrophysiology

dynamicrouting-summary

Project summary plots & tables, started for onsite retreat Jan 2024.

ecephys_etl_pipelines

Pipelines and modules for processing extracellular electrophysiology data

ecephys_spike_sorting

Modules for processing extracellular electrophysiology data from Neuropixels probes

em_aligner

A set of tools to assist in aligning (registering) large numbers of EM images into a coherent image volume in two and three dimensions.

em_aligner_python

Python version of Khaled Khairy's EM_aligner, supporting distributed assembly and solve

em_coregistration

align a 3D data set to another

em_imaging_workflow

Blue Sky workflow to support continuous processing and assembly of electron microscopy image volumes

em_stitch

EM microscopy lens correction

emc-wiki

Tracking analysis tools for interfacing with EM connectomics datasets

ephys-analysis-tools

Code base generating formatted data tables that streamlines data analysis process for ephys production metadata.

ephys-noise-analysis