Modular Remapping Model

This repository contains a Python package of the source code for the model described in this paper:

Modular Realignment of Entorhinal Grid Cell Activity as a Basis for Hippocampal Remapping

Joseph D. Monaco [1] and L. F. Abbott [2]

[1] Zanvyl Krieger Mind/Brain Institute, Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; [2] Departments of Neuroscience, and Physiology and Cellular Biophysics, Columbia University College of Physicians and Surgeons, New York, New York 10032

Hippocampal place fields, the local regions of activity recorded from place cells in exploring rodents, can undergo large changes in relative location during remapping. This process would appear to require some form of modulated global input. Grid-cell responses recorded from layer II of medial entorhinal cortex in rats have been observed to realign concurrently with hippocampal remapping, making them a candidate input source. However, this realignment occurs coherently across colocalized ensembles of grid cells (Fyhn et al., 2007). The hypothesized entorhinal contribution to remapping depends on whether this coherence extends to all grid cells, which is currently unknown. We study whether dividing grid cells into small numbers of independently realigning modules can both account for this localized coherence and allow for hippocampal remapping. To do this, we construct a model in which place-cell responses arise from network competition mediated by global inhibition. We show that these simulated responses approximate the sparsity and spatial specificity of hippocampal activity while fully representing a virtual environment without learning. Place field locations and the set of active place cells in one environment can be independently rearranged by changes to the underlying grid-cell inputs. We introduce new measures of remapping to assess the effectiveness of grid-cell modularity and to compare shift realignments with other geometric transformations of grid-cell responses. Complete hippocampal remapping is possible with a small number of shifting grid modules, indicating that entorhinal realignment may be able to generate place-field randomization despite substantial coherence.

Installation

You will need a scientific Python distribution such as Enthought Canopy or Continuum Anaconda. In the cloned repository, you can run the standard distutils installation with something like python setup.py install. The model can then be run interactively in an IPython session.

Libraries

Here is a brief description of the main modules and classes:

Top-level Modules

• dmec
  • GridCollection: grid cell population model
• place_network
  • PlaceNetwork: model simulation class
  • PlaceNetworkStd: model simulation class, search-optimized parameters
• place_network_ui
  • PlaceNetworkUI: Chaco graphical frontend for model simulation
• placemap
  • PlaceMap: spatial map class that computes place fields
• placemap_viewer
  • PlaceMapViewer: Chaco graphical interface for PlaceMap objects
• ratemap
  • CheckeredRatemap: PlaceMap subclass for rasterized simulation output
• stage
  • StagingMap: simple handler for defining and indexing the environment
• trajectories
  • RandomWalk: naturalistic random walk trajectory definition
  • BipartiteRaster: checkered rasterization defintion

Subpackages

• core
  • Base classes for models, analyses, parameter searches, and time-series data
• analysis
  • altmodels: extensions to inhibitory model
    • ModelComparison: analysis class for running model extensions
  • compare:
    • compare_AB: function that computes remapping measures
  • map_funcs: functions operating on spatial maps
  • movie:
    • SweepMovie: analysis class for creating remapping videos
  • point:
    • PointSample: analysis class for gathering statistics
  • realign:
    • RealignmentSweep: analysis class for remapping sweeps
  • scan:
    • MultiNetworkScan: analysis class for sampling parameter sweeps
  • search:
    • PlaceNetworkSearch: model parameter search definition
  • sweep:
    • SingleNetworkSweep: two-dimensional parameter sweeps
  • two_rooms:
    • SmoothRemap: analysis class for progressive remapping simulations
    • SampleRemap: analysis class for random sampling of remapping
• tools
  • A collection of scientific and utility support functions

Some of the analysis classes farm simulations out to IPython ipengine instances running on your machine. You must first start them in another terminal:

  $ ipcluster local -n C

Set C to the number of cores available on your machine.

Example Usage

You can run the model itself, specifying various parameters, or you can run pre-cooked analyses that were used as the basis of figures in the paper.

Running the model

Start IPython in -pylab mode:

$ ipython -pylab

Then, import the libraries and create a model instance:

In [0]: from grid_remap import *
In [1]: model = PlaceNetworkStd()

To see all the user-settable parameters, you can print the model:

In [2]: print model
PlaceNetworkStd(Model) object
--------------------------------
Parameters:
        C_W : 0.33000000000000002
        EC : None
        J0 : 45.0
        N_CA : 500
        done : False
        dwell_factor : 5.0
        monitoring : True
        mu_W : 0.5
        pause : False
        phi_lambda : 0.040000000000000001
        phi_sigma : 0.02
        refresh_orientation : False
        refresh_phase : False
        refresh_traj : False
        refresh_weights : True
        tau_r : 0.050000000000000003
        traj_type : 'checker'

Important model parameter definitions:

C_W            feedforward connectivity 
EC             the GridCollection to use as input
J0             gain of global inhibition
N_CA           the number of output units; each receives input from 
                    C_W*N_EC grid cells
dwell_factor   multiple of tau_r that defines raster pixel dwell time
mu_W           average weight of feedforward synapses
phi_lambda     nonlinearity threshold
phi_sigma      nonlinearity smoothness (gain)
refresh_*      orientation/phase reset per trial; new random weight
                    matrix per trial
tau_r          time constant of place-unit integration

Parameters can be changed by passing them as keyword arguments to the constructor. To simulate only 100 place units, you would call PlaceNetworkstd(N_CA=100).

Run the simulation:

In [3]: model.advance()

Look at the tracked data:

In [4]: pmap = CheckeredRatemap(model)

Running analyses

To run the figure analyses, you simply create an analysis object and run it by calling it with analysis parameters. To run progressive realignment experiments using the RealignmentSweep analysis class, you would run:

In [20]: fig = RealignmentSweep(desc='test')
In [21]: fig.collect_data?

The first command creates an analysis object with the description 'test'. The second command (with the ?) tells IPython to print out meta-data about the collect_data method. This is the method that actually performs the analysis when you call the object, so this tells you the available parameters along with their descriptions. We could run the analysis with modularity on the y-axis:

In [22]: fig(y_type='modules')

This performs the simulations, collects data for the figures, and stores data, statistics, and an analysis.log file in the analysis directory. When that completes, you can bring up the resulting figure and save it:

In [23]: fig.view()
In [24]: fig.save_plots()

Running the view method renders the figures, outputs RGB image files, and saves a figure.log file in the analysis directory. Some of the figures have parameter arguments to change the figure. You will have to use the create_plots method, as this is what the view method actually calls. To see the figure parameters and make changes:

In [25]: fig.create_plots?
In [26]: fig.create_plots(...)

The same process can be used for the other figure analysis classes. You can create your own analyses by subclassing from core.analysis.BaseAnalysis and implementing the collect_data and create_plots methods.