a toolbox for cross session sorting of neural data
- Characterize local minima in the voltage traces across the array, and obtain an estimate of overall recording quality.
- Establish a metric for individual spikes for cross session comparisons, which is robust to additive noise.
- Use a minimal temporal windows for sorting and reduce overlap between spikes
- Chronically implanted electrode arrays in awake behaving animals, with no or little electrode drift across recording sessions.
- Sorting on individual electrodes, assuming electrode distances >100 µm
- Perform clustering in a noise dependent way, and ignore bouts of high noise across the array in the clustering step.
- visualize
- roughly split into single session and cross session analysis
- use one .mat file to keep track of parameters, files etc. across sessions
- same file keeps track of which sessions have been merged
- (TODO) function that (currently) does detection and sorting for single sessions only, plus RecordingExtractors and SortingExtractors, for integration with SpikeInterface.
- (TODO) function that does the sorting for one recording session, without merging.
- script for stepwise analysis, and session merges: SortMaster.m
- extract Data and recording parameter
- extractDataFromKwik.m
- manuallyAnnotatedHdf
- remove 60 Hz component
- filter60Hz
- common average referencing
- filterCAR
- determine signal variance
and determine segments of low variance
- estimateStd
- match templates
and obtain 3D densities of local minima
- blindTemplateMatching
- find clusters
use only segments with 'low' variance
- clusterSession
- match across sessions
- mergeAll -mergeNext -mergeHash
Output structure z, saved as 'All_cat.mat', with variables
| variables for individual spikes | description |
|---|---|
| z.Spikes{id} | cluster indices of spikes for recording session 'id' |
| z.Times{id} | time stamps of spikes for recording session 'id' |
| variables for units | description |
|---|---|
| z.Channel(u,1) | Electrode site on which cluster 'u' was recorded |
| z.nSpk(id,u) | firing rate of cluster 'u' for recording session 'id' [Hz] |
| z.fracBorder(id,u) | Unit isolation: relative density of spikes in border voxels |
| z.pwt(id,u,1) | average amplitude of spikes in cluster 'u' for recording session 'id' [bins in histogram] |
| z.pwt(id,u,2) | average width of spikes in cluster 'u' for recording session 'id' [bins in histogram] |
| z.pwt(id,u,3) | average symmetry of spikes in cluster 'u' for recording session 'id' [bins in histogram] |
| z.Shapes(id,u,:) | median spike shapes ofcluster 'u' for recording session 'id' |
| z.ShapesD(id,u,:) | first and third quartile of spike shapes of cluster 'u' for recording session 'id' |
| z.Hist{id}{u} | 3D Histogram of spike shapes in cluster 'u' for recording session 'id' |
| z.Sessions(u,id) | boolean matrix for which units found in which sessions |
| Scaling | description |
|---|---|
| z.xPwr | bin edges for amplitudes |
| z.tWidth | bin centers for spike FWHM |
| z.tTail | bin centers for symmetry |
| Recording sessions | description |
|---|---|
| z.RecId{id} | Identifier of recording session 'id' (yyyy-mm-dd_hh-mm-ss) |
| z.LenRec(id) | Duration of recording session 'id' |
Output structure z, saved as 'subject_chXX_hash.mat'
| variables for individual events | description |
|---|---|
| z.hashSpikes{id} | 3D voxel locations spikes for recording session 'id' (reshape histogram as [z.Ntail x z.Nwidth x z.Namp]) |
| z.hashTimes{id} | time stamps of spikes for recording session 'id' |
####merging clusters
| parameter description | name | default value |
|---|---|---|
| threshold for JS divergence | JSthreshold | 0.2*log(2) |
| number of consecutive sessions to consider for merges | nMerge | 3 |
| acceptable range of (penalized) cross-session shifts in amplitude [bins] | Nampshift | 5 |
| acceptable range of (penalized) cross-session shifts in width [bins] | Nwshift | 1 |
| acceptable range of (penalized) cross-session shifts in symmetry [bins] | Ntshift | 1 |
| peak time of spike in shape cutouts [frames] | NcutPre | 20 |
| length of spike shape cutouts [frames] | Ncut | 60 |