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.
- aoslo-calibration-tools. Calibration routines for a three-primary Maxwellian View in our AOSLO.
- 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
Optics Resources
There are many excellent resources on the theoretical principles of AO and the design of specific systems, but less is available on the tips, tricks and protocols followed for working with AO systems. Alignment and calibration protocols for our one-photon AOSLO are available on Github at PattersonLabDocs. These are living documents and specific to our systems, but could be useful for others. Additions and feedback is welcome! Over time, we hope to include more generic documentation (e.g., finding pupil planes, coaligning lasers, etc.).
Other useful resources: