rly
Neuroscience research software engineer. Technical lead of the NWB data standard and software for neurophysiology.
Pinned Repositories
hdmf
The Hierarchical Data Modeling Framework
lindi
Linked Data Interface (LINDI) - cloud-friendly access to NWB data
nwb-schema
Data format specification schema for the NWB neurophysiology data format
pynwb
A Python API for working with Neurodata stored in the NWB Format
aibs-nwb1-to-nwb2
h5tojson
Experimental JSON-based format for HDF5 datasets
ndx-events
NWB extension to store event and TTL pulse data
ndx-pose
NWB extension to store pose estimation data
ndx-structured-behavior
An NWB extension for storing structured behavior programs and data, such as from BAABL/BEADL
simple-mua-detection
MATLAB script to detect spikes in high-pass filtered ephys data (Plexon PL2 format) using adaptive amplitude thresholding
rly's Repositories
rly/ndx-pose
NWB extension to store pose estimation data
rly/ndx-events
NWB extension to store event and TTL pulse data
rly/h5tojson
Experimental JSON-based format for HDF5 datasets
rly/ndx-structured-behavior
An NWB extension for storing structured behavior programs and data, such as from BAABL/BEADL
rly/data-reuse-stories
Examples of reuse of publicly accessible neurophysiology datasets
rly/ndx-mp4
NWB extension to store MP4 video data as bytes
rly/CaImAn
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
rly/chrome-extensions-privacy-policy
Privacy policy for the Chrome extensions that I develop
rly/dandi-cli
DANDI command line client to facilitate common operations
rly/dandi-feedstock
A conda-smithy repository for dandi.
rly/element-deeplabcut
DataJoint Element for behavioral analysis with DeepLabCut
rly/filesystem_spec
A specification that python filesystems should adhere to.
rly/hdmf-linkml
rly/hed-examples
Example Python, Matlab, and Jupyter notebook code using HED (Hierarchical Event Descriptors). Includes BIDS-compatible test datasets.
rly/jdb_to_nwb
Converts electrophysiology, photometry, and behavioral data for the hex maze task used by the Berke Lab at UCSF to NWB format.
rly/linkml-nwb-paper
rly/mesmerize-core
High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn
rly/ndx-anatomical-localization
rly/ndx-optogenetics
NWB extension for optogenetics metadata
rly/ndx-pose-feedstock
A conda-smithy repository for ndx-pose.
rly/neuroconv
Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.
rly/nwb-schema
Data format specification schema for the NWB neurophysiology data format
rly/open-bpl-new-tab
Chrome extension to add 'Open in New Tab' buttons to Berkeley Public Library Catalog search results
rly/probeinterface
Python package to handle probe layout, geometry and wiring to device.
rly/pynwb-feedstock
A conda-smithy repository for pynwb.
rly/pyout-feedstock
A conda-smithy repository for pyout.
rly/python-neo
Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats
rly/replicate-gonzalo-cogno-2023
Replication of Gonzalo Cogno et al. 2023
rly/spikeinterface
A Python-based module for creating flexible and robust spike sorting pipelines.
rly/tqdm_publisher
Subscribe to updates from tqdm progress bars with arbitrary callback functions.