Meeting Notes
- Date: 2025-06-10
- Time: 09:00 (PT)
- Location: Teams Meeting
- Presentations: @rcpeene @lrudelt @jeromelecoq
Agenda
All content should be shared one day prior to the meeting on the linked forum thread (click at the bottom of this page to upload).
- SLAP2 analysis data snapshot 1: Carter (2-3 slides)
- SLAP2 analysis data snapshot 2: Lucas (2-3 slides)
- Update on Bonsai development - python experimental launcher. Jerome, 10min.
- Discussion on stimuli changes on SLAP2 session
- Next meeting agenda
Meeting Recording
Meeting Notes
New Dataset: Carter introduced a new dataset and notebook, explaining the files and their usage, and recommended using DFF for analysis to account for bleaching.
Dataset Introduction: Carter introduced a new dataset available on Dandi, which includes files with F0, DF, and DFF. He explained that these files are named accordingly and can be accessed directly from the provided paths.
Notebook Explanation: Carter explained the new notebook added to the website, which sets up the environment, downloads the files, and allows users to run the analysis out-of-the-box. He recommended viewing the notebook on GitHub for better rendering.
File Details: Carter detailed the contents of the files: DF is the preprocessed recording of fluorescence, F0 is the baseline fluorescence metric, and DFF is the trace accounting for the baseline. He provided code to reproduce F0 and DFF using a median filter and rolling window operations.
Analysis Recommendation: Carter recommended performing all analyses using DFF to account for the decrease in fluorescence due to bleaching. Jerome supported this recommendation, emphasizing the importance of considering bleaching in the analysis.
Analysis Presentation: Lucas presented his analysis on calcium imaging and contextual modulation, highlighting the variability in responses and the need for further statistical testing.
Analysis Overview: Lucas presented his analysis on calcium imaging, focusing on contextual modulation of responses. He aimed to reproduce previous findings on calcium imaging of somas and modulation of responses for deviant and redundant oddballs.
Findings: Lucas found variability in responses, with some enhancement and suppression observed. He noted a lack of depression for standard stimuli, which was surprising compared to previous studies on layer 2-3 and layer 5 cells.
Statistical Testing: Lucas emphasized the need for further statistical testing, including proper multiple comparison correction, to validate the observed effects. He suggested linking the analysis to other studies and disentangling long-term changes from contextual modulation.
Discussion Points: Jerome and Karim raised questions about the speed of depression and the importance of trial order and intervals. Lucas agreed to consider these factors in further analysis and to reach out to Jordan for additional insights.
Stimulus Design: Jerome and Lucas discussed potential changes to the stimulus design, including the need for control conditions and the importance of statistical power analysis.
Control Conditions: Jerome and Lucas discussed the need for control conditions to compare responses with and without oddballs. They suggested having orientation blocks without oddballs to serve as a control for the experiment.
Statistical Power: Jerome emphasized the importance of conducting a statistical power analysis to determine the number of trials needed to measure responses accurately. Lucas agreed to perform sub-sampling analysis to assess the impact of trial numbers on statistical results.
Design Changes: Lucas proposed several changes to the stimulus design, including enforcing a minimum number of repetitions before presenting a deviant stimulus and reducing the number of trials to fit the experiment within a reasonable timeframe.
Next Steps: Jerome proposed starting a discussion thread on the next stimulus design iteration, including a PowerPoint with potential changes and statistical power analysis to guide decisions. Lucas agreed to contribute to this effort.
Bonsai Development: Jerome demonstrated the new bonsai launcher script, which automates the deployment and execution of bonsai workflows across multiple machines.
Launcher Script: Jerome demonstrated the new bonsai launcher script, which automates the deployment and execution of bonsai workflows. The script downloads bonsai, installs necessary packages, and executes the workflow based on a JSON configuration file.
Deployment Process: Jerome explained the deployment process, which includes fetching rig parameters, cloning the repository, and downloading the required packages. The script ensures that the correct version of bonsai and the workflow are executed on each machine.
Packaging Outputs: Jerome described the packaging process, where the output of bonsai is saved and organized into a package. This package includes the data and parameters used in the experiment, ensuring reproducibility and traceability.
Future Development: Jerome mentioned ongoing development of C# plugins to interface with specific hardware and the creation of Python scripts for different oddball types. These developments aim to streamline the deployment of experiments across multiple rigs.