Meeting Notes
- Date: 2025-05-13
- Time: 09:00 (PT)
- Location: Teams Meeting
- Facilitator: @jeromelecoq
Agenda
- Introduce resources on bonsai development.
- Discuss progress on standard-oddball stim.
- Go through bonsai workflow.
- Discuss parameters.
- Discuss progress on sensory-motor stim, go through bonsai workflow.
- Go through bonsai workflow.
- Discuss parameters.
- Discuss duration oddball workflow state.
- Discuss potential plan for replication and validation outside of Allen.
Meeting Recording
Notes
Introduction to Bonsai and Resources
-Jerome introduced Bonsai and reviewed the available resources, including a tutorial video. -Emphasis was placed on deploying and testing Bonsai workflows independently from specific hardware configurations. -Participants were encouraged to download the Bonsai package and run the stimulus workflows on their own rigs for validation and feedback.
Gamma Correction and Screen Calibration
-Alex raised concerns about variations in monitor output and the need for gamma correction to ensure consistent visual presentation across labs. -Jerome confirmed this is already being addressed. A gamma calibration workflow using a photodiode is in progress. -There was also discussion about screen geometry and viewing distance, which can be configured in the "Orthographic Group" section of the Bonsai script. Inputting correct screen geometry allows spatial frequency and gamma to be properly adjusted. -Alex suggested adding a marker or comment in the script to remind users to input these parameters.
Stimulus Testing
-Jerome demonstrated how to access and run the standard oddball stimulus in Bonsai. -The workflow was tested on SLAP2, where receptive fields were observed confirming effective stimulus delivery. -A bug affecting temporal alignment between stimulus and recorded data (due to MATLAB-to-Python conversion) was fixed. Now, all data are aligned to a common clock in NWB. -Alex inquired about hardware compatibility and whether teams need to use the same components. -Jerome clarified that although some stimulus elements rely on SLAP2-specific hardware, alternative components will be recommended for broader use. -The standard oddball stimulus is nearly finalized, and Jerome encouraged labs to test it and report any issues. -Sensory motor oddball design was introduced, which links the wheel encoder to gratings and allows presentation of additional visual elements. -Alex, Kaspar, and Karim discussed possibilities for varying speed/gain and adding more oddball types. -Jerome recommended starting a discussion thread on the website to coordinate design decisions and statistical considerations.
Workflow Replication Across Labs
-The team emphasized the importance of standardizing stimuli across labs to ensure reproducibility and avoid compatibility issues. -Jerome noted Bonsai’s advantage in simplifying closed-loop coding, which is crucial for more interactive designs. -While alternative software can be used, extreme care must be taken to ensure consistency. -Forum threads were encouraged for sharing ideas and troubleshooting collectively. -Jerome will grant GitHub ticketing access to anyone who provides their username.
Project Updates and Next Steps
-Current tickets include gamma calibration and finalization of mismatch and sensory motor workflows. -Two new SLAP2 datasets will be uploaded to DANDI soon. -Sarah has begun work on the duration oddball, which will be piloted at the Allen Institute. -Alex was asked to continue validating the standard oddball workflow. -Karim is interested in the sensory motor stimulus but still awaiting required hardware. Setup is expected to take some time. -Karim asked about running entire experiments locally versus using SLAP2 as a starting point. -It was noted that sensory motor experiments are not currently planned for SLAP2 due to their complexity and training requirements.
2. Open Discussion and Q&A
- [Summarize key points discussed and questions raised.]
Next Steps and Action Items
Next week’s meeting will focus on SLAP2 analysis.