DANDI Atlas Explorer
A browser-based 3D viewer for finding data in the DANDI Archive by brain region. Regions are drawn from standard reference atlases and shaded by how many dandisets touch them, and clicking one isolates it and lists the associated datasets with direct links. It currently covers five atlases across three species, including the Allen CCF for mouse. The region assignments come from metadata in the NWB files themselves and are refreshed daily as the archive grows. We built the viewer, and it is maintained under the DANDI organization.
GuPPy
Guided Photometry Analysis in Python, a free and open-source fiber photometry analysis tool developed in collaboration with the Lerner Lab at Northwestern University. GuPPy covers artifact correction, signal normalization, peak detection, and visualization. The Lerner Lab leads the scientific development, while our team at CatalystNeuro works on the software engineering foundation that makes GuPPy sustainable and accessible, including installation and distribution, automated quality assurance, reliability and error handling, and data sharing across research platforms.
Neurosift
A browser-based viewer for NWB files, developed at the Flatiron Institute. Neurosift opens datasets directly from the DANDI Archive, EMBER, and OpenNeuro without downloading them, and renders what it finds as interactive views, including spike raster plots, peristimulus time histograms aligned to trial events, two-photon imaging series, and pose estimation superimposed on the behavioral video. A pip-installable command serves local files to the same interface at neurosift.app. We are among its largest contributors outside Flatiron, and we use it throughout our conversion work, since sharing a link is the quickest way for a lab to see what its converted data actually contains.
Neo
Neo is a package for reading electrophysiology data in Python, writing data, and manipulating them. Neo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology. We use neo as part of our data conversion pipeline, and contribute to it, ensuring it continues to efficiently read the latest modern acquisition data formats. We also collaboratively manage a library of test electrophysiology files that was started by the neo development team and is now also used by SpikeInterface and NeuroConv.
SpikeInterface
A unified framework for spike sorting analysis and comparison. We contribute to this community-driven project that aims to standardize and simplify spike sorting workflows.
torch_brain
torch_brain is a Python library for various deep learning models designed for neuroscience. We contribute to this open-source project that provides tools for building and training AI models tailored to neuroscience data.
VAME
A deep learning framework for behavioral clustering and analysis. We contribute to this open-source project that enables automated analysis of animal behavior from video data.
Voluseg
A platform for volumetric segmentation of calcium imaging data. We contribute to this collaborative project that provides tools for analyzing and processing large-scale neural imaging datasets.
