tmchartrand
commented
2 years ago @ru57y34nn these ideas look great, and I'm sure we'll talk at some point soon about the logistics of integrating this, but figured I'd comment now with one point that might help us spec out that future work. You may have already thought through this, but to me the main question is which existing classes can be adapted to process this sweep, i.e. whether the functionality in spike_detector.py will work with the voltage-clamp cell-attached sweep (possibly with modified parameters).
If you get a chance, it might be worth playing around with that a bit, and seeing where it works/fails, and in particular trying the sequence of calls that the SpikeFeatureExtractor uses:
putative_spikes = spkd.detect_putative_spikes(v, t, self.start, self.end,
dv_cutoff=self.dv_cutoff,
dvdt=dvdt)
peaks = spkd.find_peak_indexes(v, t, putative_spikes, self.end)
putative_spikes, peaks = spkd.filter_putative_spikes(v, t, putative_spikes, peaks,
self.min_height, self.min_peak,
dvdt=dvdt)
ru57y34nn
gouwens
Describe the use case that is addressed by this feature. The problem that this feature would solve.
IVSCC is patching in subcortical brain regions where cells are more likely to exhibit spontaneous firing. Spontaneous firing data is acquired by adapting the cell-attached/gigaohm seal (EXTPCllATT) stimulus set to include an additional 60 seconds at the end of the sweep. The two main advantages of amending the cell-attached sweep are:
(1) The physiological spontaneous firing behavior is maintained because cell-attached mode does not alter the internal ionic composition of the neuron.
(2) The probability of successfully acquiring the data before a spontaneous break-in is increased relative to acquiring the data in a separate sweep that comes after EXTPCllATT.
The ability to use EXTPCllATT for seal QC is maintained.
By enhancing IPFX to analyze the spontaneous firing behavior recorded in EXTPCllATT, spontaneous firing behavior can contribute to cell-type classification.
We expect the spontaneous firing rates of cells to be higher than normal at the beginning of a EXTPCllATT sweep because the potassium in the internal solution is discharged while approaching the cell with positive pressure on the pipette. After sealing onto the cell, the elevated external potassium will dissipate. The proposed analysis captures the spontaneous firing rate after the potassium concentration has stabilized.
Describe the solution you'd like What you want to happen.
Add spontaneous firing feature extraction to IPFX for the EXTPCllATT sweep. The first 300 ms of the sweep are unchanged and are still used to measure the value of the seal, but we would like to perform the following analysis steps on the last 60 seconds of the sweep:
• Filter the sweep (low pass filter) to improve spiking SNR • Remove exponential change in baseline current due to changing seal resistance (when present) • Perform spike detection (in voltage-clamp) • Measure the instantaneous spike rate throughout the sweep • Determine when or if steady-state firing is reached? o Is 60 seconds long enough? • Extract features from sweep o Steady-state firing rate (physiological spontaneous firing rate) o Change in Instantaneous firing rate over the duration of the sweep o Min and max instantaneous firing rates o Instantaneous rate vs. subsequent rate
Describe alternatives you've considered Any alternative solutions or features you've considered.
Additional context Add any other information about the feature request here.
Do you want to work on this issue? Are you willing and able to work on this feature? If so, let us know here (and see the guide). Thank you!
I am willing to work on this request along with others from the Ephys team.