Open Source Code

We have developed a number of tools to support our research and make them available to the community. These include:

• SBFSEM-tools. A MATLAB toolbox for 3D rendering and analysis of connectomics data with serial block-face scanning electron microscopy. The underlying classes are generic and likely applicable to many techniques. Specialized support is included for disc-based annotations (e.g., from the open-source Viking annotation software), SWC, and accessing SQL annotation databases through OData queries. A smaller set of tools for Python (py-sbfsem) is also available.
• AOData. A framework for managing data, metadata and code for adaptive optics imaging experiments.
• h5tools-matlab. High-level interface for working with the low-level HDF5 library in MATLAB. Adds support missing from MATLAB's built-in HDF5 functions (e.g., groups, links, and compound data types).
• RoiViewer. Standalone user interface for viewing ROI responses and experimenting with common signal processing strategies. An streamlined version for use during an experiment is also available (faoslo-online).
• facile-tools. A large MATLAB toolbox containing a variety of functions for working with Functional Adaptive-optics Calcium Imaging in the Living Eye.

Publication Data and Code

Repositories containing compiled software and unprocessed data:

• Patterson_Neitz archive on Neuromorpho. Morphological data (in SWC format) from my connectomics and confocal microscopy work on S-OFF midget RGCs, M1 ipRGCs, M2 ipRGCs, small bistratified RGCs, and ON dsRGCs in the Neitz lab is available on Neuromorpho. The data includes 2 horizontal cell types, 3 bipolar cell types, 3 amacrine cell types, and 5 ganglion cell types.
• Chromatic and Spatial Tuning archive on OSF. Data, software, and Tyler's processing pipeline for Godat et al (2022) PLoS ONE

Github repositories containing analysis code and 3D reconstructions:

• NonCardinalRGCs. Godat et al (2024) Journal of Neuroscience.
• Smooth Monostratified RGCs. Patterson, Girresch, et al. (2024) ENeuro
• SConeEdgeDetection. Patterson et al (2019) Scientific Reports
• SynapticInputsToOnParasols. Patterson, Bordt et al (2019) Journal of Comparative Neurology
• RabbitGammaCell. Bordt et al (2019) Visual Neuroscience