Meeting Notes
- Date: 2025-09-16
- Time: 09:00 (PT)
- Location: Teams Meeting
- Presentations: @jeromelecoq
Agenda
- Quick follow-up on review at Physiological Review. Q&A
- Presentation on plans for imaging data.
- Discussion on how to best classify cells.
Meeting Recording
Meeting Notes
Physiological Review Manuscript Status and Authorship: Jerome updated the group on the status of the physiological review manuscript, including the addition of Henry Kennedy as a senior corresponding author and the need for all coauthors to clarify their contributions in a shared Google Sheet.
Editorial Board Feedback: Jerome informed the group that the editorial board of the Physical Review requested the addition of more senior corresponding authors, leading to the inclusion of Henry Kennedy, who agreed to participate as a senior co-author.
Contribution Table Update: Jerome asked all coauthors to update a Google Sheet with their specific contributions to the manuscript, moving beyond the previous alphabetical listing to provide a clearer record of individual roles.
Experimental Design for Imaging and Neuropixels Data: Jerome presented the current experimental design for imaging and neuropixels data, outlining the use of multiple sensory prediction contexts, complementary technologies, and the plan to record both excitatory and inhibitory neurons using a pan-neuronal line.
Experimental Contexts and Technologies: Jerome described the plan to record from two cohorts (imaging and neuropixels) across four different sensory prediction contexts (sensory motor, standard, oddball, sequential, and temporal jitter), leveraging the complementary strengths of two-photon imaging (high spatial resolution) and neuropixels (high temporal resolution).
Integration of SLAP2 Data: Jerome mentioned ongoing discussions with the SLAP2 team to include SLAP2 data, which would provide high temporal and spatial resolution at a smaller scale, further complementing the existing technologies.
Use of Pan-Neuronal Line: The group decided to use a pan-neuronal GCaMP line to record both excitatory and inhibitory neurons in the same animal, allowing for dense sampling and integration of network activity, but raising the challenge of distinguishing cell types post hoc.
Strategies for Cell Type Classification in Imaging Data: Jerome led a discussion with Alexander, Jordan, Farzaneh, and others on methods for classifying cell types in imaging data, evaluating functional, anatomical, and transcriptomic approaches, and considering the feasibility and resource requirements of each.
Functional Classification Approaches: Jerome and others discussed using functional response properties, such as contrast sensitivity and orientation tuning, to distinguish cell types (e.g., VIP, SST, PV neurons), referencing studies from the Allen Institute and considering the discriminability of these features.
Anatomical and Transcriptomic Methods: The group considered linking imaging data with existing electron microscopy (EM) datasets and spatial transcriptomics as more definitive classification methods, but noted significant resource and technical barriers to implementing these approaches in the current project.
Optogenetic and Electrophysiological Markers: Martin and Alexander discussed the use of optogenetic tagging and electrophysiological features (e.g., firing patterns, response to flicker) to help classify inhibitory neuron subtypes, particularly in neuropixels recordings.
Limitations and Ground Truth Challenges: Participants debated the concept of 'ground truth' in cell type classification, acknowledging the limitations of each method and the gradient nature of biological markers, with Alexander emphasizing the value of EM and transcriptomics for more definitive identification.
Selection and Design of Visual Stimuli for Cell Type Mapping: Jerome, Alexander, Jordan, and Farzaneh discussed the selection and adaptation of visual stimuli (Trippy, Zebra) for mapping cell types, aiming to leverage existing datasets and optimize contrast levels for functional classification in upcoming pilot experiments.
Stimulus Comparison and Rationale: The group compared the Trippy and Zebra stimuli, noting their similarities and differences in spatial frequency content and their relevance to previous EM and functional studies, with the goal of maximizing compatibility and interpretability.
Contrast Level Variations: Participants agreed on the importance of including multiple contrast levels (very low, intermediate, and high) in the stimulus design to better differentiate cell types, particularly VIP neurons, based on their contrast sensitivity.
Pilot Experiment Planning: Jerome proposed integrating both Trippy and Zebra stimuli with varying contrasts into the upcoming neuropixels pilot, with Alexander offering to help generate and test the stimulus videos for deployment on the experimental rig.
Code and Implementation Logistics: The group discussed the availability of code for generating the stimuli, with Alexander noting that Trippy's code is not yet published but could be recreated, and Jerome planning to request access from the original authors.
Future-Proofing Tissue for Advanced Analyses: Jordan and Jerome discussed the possibility of preserving tissue from key experiments for future EM or transcriptomic analysis, acknowledging technical challenges and the need for further consultation with experts.
Tissue Preservation for EM: Jordan inquired about preserving tissue for potential future EM reconstruction, with Jerome agreeing to investigate the feasibility and storage requirements, and Sara noting in the chat that storage is possible but not trivial.
Transcriptomic Analysis Limitations: Jerome explained that transcriptomic analysis requires timely processing due to staining limitations, making long-term storage less feasible compared to EM.
Progress and Next Steps for SLAP2 and Data Analysis: Jerome, Alexander, Andrew, and Lucas reviewed the current status of SLAP2 data collection and analysis, confirming the inclusion of calcium imaging data, discussing analysis tools, and outlining plans for internal alignment and future presentations.
SLAP2 Data Status: Andrew clarified that calcium imaging data is included in Channel 2 of the SLAP2 datasets, with the best indicator lifetime being approximately 20 minutes, and that both soma and dendrite signals are available for some recordings.
Analysis Tools and Progress: Alexander reported developing code for quick plotting of responses in the fixed files and expressed interest in analyzing the calcium data further, while Lucas confirmed the availability of recent datasets for planned analyses.
Internal Planning and Future Presentations: Jerome mentioned ongoing internal discussions to finalize the SLAP2 data collection plan and announced the intention to invite Dimitri Yatsenko to present on Trippy stimulus analysis in an upcoming meeting.