Author: Lydia Ng @ Janelia NWB hackathon- User days 05/14/2019
- Peter Petersen ([email protected])
- Roman Husazar ([email protected])
Peter and Roman are experimentalists that are doing variations of similar experiment generating extracellular recording on free moving rat and mice. Neural activity is recorded from implanted probes as the rat/mouse is sleeping and/or doing a spatial track task.
The probe is implanted based on bregma coordinates using an atlas (such as Paxinos or Swanson). Spike sorting is required to process the raw data files into spike times for individual cells. Cells in different layer of the hippocampus have stereotypical response signature, which can be used to classify and annotate the cells. Postmortem histology using different stains is sometimes done to confirm the anatomical location of the probes.
The rodent is either put into the sleep box for resting or into the track apparatus. They will typically switch on recording as the rodent starts the one of these activities. There is no recording while the mouse is in between activities.
Color video of the rodent moving round in the maze is also obtained. The spatial location of the mouse is computed by processing the video and modeling the motion as rigid body.
Several track layout was described: linear, W (or E) and circular. Example track task is alternation in the W layout. Finishing the entire lap constitute a trial for analysis
The track task could also include manipulation such as optogenics or stimulation such as an air puff or light based on contingencies (eg, when the mouse is at specific location).
The most important aspect to consider for using someone else’s data is knowing something about the data quality.
Roman indicated he may want to use similar dataset to study ripples.
Within a dataset, there is a need for tools to search the data for specific events (eg ripples) or states (eg mouse is asleep or in the home cage) for inclusion or exclusion in downstream analysis.
Peter is building the Buzsakilab.com data inventory and portal currently covering 500TB of data. The database has been built in WordPress. The key data models include: experimenter, subject, types of probes, implants, surgeries, what type of behavior.
[] Email Peter to either access the buzsakilab.com portal or to access the different data tables schema/attributes and example data
| Entity | Information |
|---|---|
| Species | Rat and mouse |
| Genetic Tools | n/a |
| Devices | Implanted probes |
| Spatial coordinates & anatomy | Bregma coordinates for probe insertion. Use LPF and cell density profile to further refine probe location |
| Target areas | hippocampus |
| Appartus | Linear, W or circular track |
| Stimulus | Air puff |
| Manipulation | optogenics |
| Behavior | Complete the track task in certain order to obtain a reward |