Allen Institute for Neural Dynamics's Projects
Repo for Ophys utils
Evaluating Registration and Stitching
User-friendly tools for accessing paths, metadata and assets related to AIND sessions
AIND-specific access to data stored in SLIMS
Auto-generated python code to interface with the slurm cluster
Wrapper around smartsheet python api
Code for classifying the cell candidate outputs from aind-smartspim-segmentation within smartspim pipeline
Data transformations applied to the SmartSPIM data before uploading to the cloud storage service.
Image processing capsule to remove streaks from light-sheet images.
SmartSPIM evaluation capsule
Performs large-scale flatfield correction using zarr format
SmartSPIM module to generate OMEZarr data from fused images
Creates max intensity projections (MIPs) from light sheet volumes across all three axes
Repository that hosts the SmartSPIM pipeline code
Takes the output of segmentation and ccf registration to calculate cell counts per brain region
segmentation module for SmartSPIM cloud pipeline
Stitching and fusion pipeline in the cloud
Data validation scrips for the SmartSPIM data.
Code for the ventricle segmentation problem
Repository that takes the spots from a single channel and obtains statistics from other channels
Capsule to load and interact with the Visual Behavior 2P dataset
Data staging service that prepares acquistion data for cloud upload to Amazon S3 and Code Ocean processing.
Scripts to detect spots on Z1 data
A repository for the aind-bci-no-movement experiment
A repository for the aind-change-detection task experiment
A repository with core primitives for analysis shared across `Aind.Behavior` tasks