v1.7.1

• Updates gettingStarted script
• Updates GUI for more robust visualization
• Fixes bug in non-somatic UpSet output, where some units were wrongly not classified as non-somatic

v1.7.0

A bunch of things because I haven't done a release in a while:

New features:

• support for post-hoc splitting/merging in phy - bombcell can now run on those new outputs. This introduced a breaking change - the loadEphys function now needs an additional input to work properly - see the gettingStarted.mlx script
• option to fit spatial decay with an exponential function - this is now the default, it performs much better
• better non-somatic metrics: we now have two ratios, the initial peak to repolarization peak ratio and the main peak to trough ratio
• introduces a new noise metric: the repolarization peak to trough ratio
• another (slightly better but slower) option to compute refractory period violations: Llobet et al. set param.hillOrLlobetMethod to 0 / false to enable.

Visualization update:

• updated GUI to be in two parts, with dynamic histograms that show where the current unit falls in the distribution. Helpful to adjust and fine-tune parameters

Fixes:

• only compute spatial decay of geometry of probe allows (ie if it is a high density probe)
• more robust waveform peak and trough detection

v1.6.0

• more robust spatial decay computation: template values are optionally (if param.normalizeSpDecay is set to 1) normalized relative to the peak value, making the spatial decay slope calculation more robust. - thanks @cbimbo for the suggestion. To update previously computed values, see the function bc_updateSpatialDecaySlope

• distance metric bug fix - thanks @chrisan97

v1.5.0

Handles kilosort4 spike sorting output.

v1.4.0

Added feature: option to fine-tune the non-somatic classification. Now, if a unit has a its largest detected peak before the trough, it is no longer automatically classified as non-somatic. The peak needs to be param.firstPeakRatio times larger than any value after the waveform's trough. Thanks @LaurenzMuessig .

Fixed a bug in classifying MUA unit. Thanks @JRegg66.

v1.3.0

New module to compute a host of ephys parameters and to classify striatal and cortical units.

v1.2.0

New option to separate non-axonal spikes into MUA and good. Thanks @cbimbo !

If param.splitGoodAndMua_NonSomatic is set to 1, non-somatic units are further separated into non-somatic multi-unit and non-somatic good unit.

Bombcell v1.1.0

Added features:

• New option to remove duplicate spikes. if param.removeDuplicateSpikes is true, for any pairs of spikes on the same channel that are within param.duplicateSpikeWindow_s of each other, the lowest amplitude spike or the spike belonging to the cluster with the least spikes is removed. see MouseLand/Kilosort#29 for a discussion on duplicate spikes in Kilosort.

• Better back-compatibility management. Introduced the function bc_checkParameterFields that checks the inputed parameter structure/table has all necessary fields. This code adds any missing fields with values resulting in the same behavior as before any new feature or feature flag was added.

Bombcell v1.0.1

• Optional compatibility with phy. If param.saveAsTSV is true, bombcell saves a tsv file per quality metric in the param.ephysKilosortPath path. This needs to be the same path as where all your kilosort output paths are saved.

• Move makepretty function to a separate repo, so it can be easily used across different projects. Users now need to download https://github.com/Julie-Fabre/prettify_matlab and add it to their matlab path.

• Other minor bug fixes