Place Cells

Understanding spatial reasoning

What is a place cell?

Source: Ryan Jones

  • Pyramidal neuron typically located in CA1 or CA3
  • Attenuate firing with changes in spatial location
  • Circuitry to be discussed
  • Role in spatial learning, decision making and memory encoding

Sharp Wave Ripples (SWRs)

raw LFP

ripple band filtered

SWR

CA1 propagates to CA3, to produce SWRs

Adapted from Laura Colgin

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

Place Cells

By Ariel Feldman

Place Cells

A quick, comprehensive overview of what place cells are and how they function.

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