Rhythms of the Hippocampal Network             

Laura Lee Colgin, Nature Reviews 2016

Plus a lil bit of REL

& More

The Hippocampal Structures

The Hippocampal Neurons

Stellate neurons

Pyramidal neurons

Granule neurons

What is a place cell?

Source: Ryan Jones

  • Pyramidal neuron typically located in CA1 or CA3
  • Attenuate firing with changes in spatial location (one location)
  • No topographic layout
  • Remapping in novel environments
  • Influenced by visual, tactile, olfactory, etc. cues

What's the difference?

Encoding in 3D

Wohlgemuth, Yu & Moss

Rhythms of the hippocampal network

Theta

Sharp-wave ripples (SWRs)

Gamma

  • ~4-12 Hz
  • ~150-250 Hz
  • Slow ~22-55 Hz
  • Fast ~60-100 Hz

Theta Oscillations

  • Formation of sequential memories
  • Allows brain to accept new information
  • Observed during activity and REM
  • Septum impacts firing in DG, CA1 & CA3
  • Required for memory, not place fields

Theta Oscillations

  • Theta sequences
  • Ordered spikes; locations traveled
  • Experience-dependent, meaningful concepts
  • Disruption prevents memory of sequence

Theta Oscillations

Baseline

Disruption

Return to normal

Gamma Oscillations

  • Slow gamma driven by CA3, fast driven by EC
  • Fast gamma related to current trajectory and recent locations
  • Slow gamma retrieves spatial memories from CA3 network
  • Upcoming locations when re-running
  • Reflect inhibitory events in CA1, CA3 & DG

Gamma Oscillations

  • Theta and gamma couple to each other
  • Phase-locking observed both in awake and REM

Gamma Oscillations

Sharp Wave Ripples (SWRs)

raw LFP

ripple band filtered

SWR

CA3 propagates to CA1, to produce SWRs

Adapted from Laura Colgin

Responsible for consolidation of spatial memories

def sosfiltfilt(timeseries, *, fl=None, fh=None, fs=None, inplace=False, bandstop=False,
                gpass=None, gstop=None, ftype=None, buffer_len=None, overlap_len=None,
                parallel=True,
                **kwargs):
                # make sure that fs is specified, unless AnalogSignalArray is passed in
                if isinstance(timeseries, (np.ndarray, list)):
        if fs is None:
            raise ValueError("Sampling frequency, fs, must be specified!")
        elif isinstance(timeseries, core.RegularlySampledAnalogSignalArray):
            if fs is None:
                fs = timeseries.fs
        else:
            raise TypeError('Unsupported input type!')

        try:
            assert fh < fs, "fh must be less than sampling rate!"
        except TypeError:
            pass
        try:
            assert fl < fh, "fl must be less than fh!"
        except TypeError:
            pass

        if inplace:
            out = timeseries
        else:
            out = deepcopy(timeseries)
        if overlap_len is None:
            overlap_len = int(fs*2)
        if buffer_len is None:
            buffer_len = 4194304
        if gpass is None:
            gpass = 0.1 # max loss in passband, dB
        if gstop is None:
            gstop = 30 # min attenuation in stopband (dB)
        if ftype is None:
            ftype = 'cheby2'

        try:
            if np.isinf(fh):
                fh = None
        except TypeError:
            pass
        if fl == 0:
            fl = None

        # Handle cutoff frequencies
        fso2 = fs/2.0
        if (fl is None) and (fh is None):
            raise ValueError('Nonsensical all-pass filter requested...')
        elif fl is None: # lowpass
            wp = fh/fso2
            ws = 1.4*fh/fso2
        elif fh is None: # highpass
            wp = fl/fso2
            ws = 0.8*fl/fso2
        else: # bandpass
            wp = [fl/fso2, fh/fso2] 
            ws = [0.8*fl/fso2,1.4*fh/fso2]
        if bandstop: # notch / bandstop filter
            wp, ws = ws, wp

        sos = sig.iirdesign(wp, ws, gpass=gpass, gstop=gstop, ftype=ftype, output='sos', **kwargs)

        # Prepare input and output data structures
        # Output array lives in shared memory and will reduce overhead from pickling/de-pickling
        # data if we're doing parallelized filtering
        if isinstance(timeseries, (np.ndarray, list)):
            temp_array = np.array(timeseries)
            dims = temp_array.shape
            if len(temp_array.shape) > 2:
                raise NotImplementedError('Filtering for >2D ndarray or list is not implemented')
            shared_array_base = Array(ctypes.c_double, temp_array.size, lock=False)
            shared_array_out = np.ctypeslib.as_array(shared_array_base)
            # Force input and output arrays to be 2D (N x T) where N is number of signals
            # and T is number of time points
            if len(temp_array.squeeze().shape) == 1:
                shared_array_out = np.ctypeslib.as_array(shared_array_base).reshape((1, temp_array.size))
                input_asarray = temp_array.reshape((1, temp_array.size))
            else:
                shared_array_out = np.ctypeslib.as_array(shared_array_base).reshape(dims)
                input_asarray = temp_array
        elif isinstance(timeseries, core.RegularlySampledAnalogSignalArray):
            dims = timeseries._data.shape
            shared_array_base = Array(ctypes.c_double, timeseries._data_rowsig.size, lock=False)
            shared_array_out = np.ctypeslib.as_array(shared_array_base).reshape(dims)
            input_asarray = timeseries._data

        # Embedded function to avoid pickling data but need global to make this function
        # module-visible (required by multiprocessing). I know, a bit of a hack
        global filter_chunk
        def filter_chunk(it):
            """The function that performs the chunked filtering"""

            try:
                start, stop, buffer_len, overlap_len, buff_st_idx = it
                buff_nd_idx = int(min(stop, buff_st_idx + buffer_len))
                chk_st_idx = int(max(start, buff_st_idx - overlap_len))
                chk_nd_idx = int(min(stop, buff_nd_idx + overlap_len))
                rel_st_idx = int(buff_st_idx - chk_st_idx)
                rel_nd_idx = int(buff_nd_idx - chk_st_idx)
                this_y_chk = sig.sosfiltfilt(sos, input_asarray[:, chk_st_idx:chk_nd_idx], axis=1)
                shared_array_out[:,buff_st_idx:buff_nd_idx] = this_y_chk[:, rel_st_idx:rel_nd_idx]
            except:
                raise ValueError(("Some epochs were too short to filter. Try dropping those first,"
                                  " filtering, and then inserting them back in"))

        # Do the actual parallellized filtering
        if (sys.platform.startswith('linux') or sys.platform.startswith('darwin')) and parallel:
            pool = Pool(processes=cpu_count())
            if isinstance(timeseries, (np.ndarray, list)):
                # ignore epochs (information not contained in list or array) so filter directly
                start, stop = 0, input_asarray.shape[1]
                pool.map(filter_chunk, zip(repeat(start), repeat(stop), repeat(buffer_len),
                                         repeat(overlap_len), range(start, stop, buffer_len)),
                                        chunksize=1)
            elif isinstance(timeseries, core.RegularlySampledAnalogSignalArray):
                fei = np.insert(np.cumsum(timeseries.lengths), 0, 0) # filter epoch indices, fei
                for ii in range(len(fei)-1): # filter within epochs
                    start, stop = fei[ii], fei[ii+1]
                    pool.map(filter_chunk, zip(repeat(start), repeat(stop), repeat(buffer_len),
                             repeat(overlap_len), range(start, stop, buffer_len)),
                             chunksize=1)
            pool.close()
            pool.join()
        # No easy parallelized filtering for other OSes
        else:
            if isinstance(timeseries, (np.ndarray, list)):
                # ignore epochs (information not contained in list or array) so filter directly
                start, stop = 0, input_asarray.shape[1]
                iterator = zip(repeat(start), repeat(stop), repeat(buffer_len),
                               repeat(overlap_len), range(start, stop, buffer_len))
                for item in iterator:
                    filter_chunk(item)
            elif isinstance(timeseries, core.RegularlySampledAnalogSignalArray):
                fei = np.insert(np.cumsum(timeseries.lengths), 0, 0) # filter epoch indices, fei
                for ii in range(len(fei)-1): # filter within epochs
                    start, stop = fei[ii], fei[ii+1]
                    iterator = zip(repeat(start), repeat(stop), repeat(buffer_len),
                                   repeat(overlap_len), range(start, stop, buffer_len))
                    for item in iterator:
                        filter_chunk(item)

        if isinstance(timeseries, np.ndarray):
            out[:] = np.reshape(shared_array_out, dims)
        elif isinstance(timeseries, list):
            out[:] = np.reshape(shared_array_out, dims).tolist()
        elif isinstance(timeseries, core.RegularlySampledAnalogSignalArray):
            out._data[:] = shared_array_out

        return out

Nelpy Filtering

Why do we need prediction?

  • Missing approx. 40-60% of the SWR
    • Never interrogated ripple generation
    • Validation of in vivo interaction
  • Research context
    • Interact with memory recall & consolidation
    • Analyze impact on decision-making

Objective

Design Challenges

Goal: Apply machine learning techniques towards building a realtime closed loop SWR detection & disruption system.

  • Anomalous event
    • Ripples happen rarely
    • Complex classification problem
  • Loss value
    • ​Weighting loss misclassifications
    • Custom function
  • Must be realtime applicable

Spectral Domain

Sensitivity

Convolutional vs. Recurrent

\frac{TP}{TP + FN}
\frac{TN}{TN + FP}

Convolutional Architecture

Multi-Layer Perceptron

CA1

CA2

CA3

Convolutional Architecture

How will we approach this?

  • Boosting & Cascade Learning
    • Multiple mediocre classifiers

Why do we care?

  • Memory Enhancement
    • ​Cortical p-waves & theta
  • Greater Understanding of Consolidation
    • ​How do we improve learning?
    • Neural basis of memory disorders
  • Post-Traumatic Stress Disorder
    • ​Remove access to specific memories
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