ratinabox 1.0.1

RatInABox: A package for simulating motion and ephys data in continuous environments

RatInABox

RatInABox (paper here) is a toolkit for generating locomotion trajectories and complementary neural data for spatially and/or velocity selective cell types.

With RatInABox you can:

• Generate realistic trajectories for rats exploring complex 1- and 2-dimensional environments under a smooth random policy, an external control signal, or your own trajectory data.
• Generate artificial neuronal data Simulate various location or velocity selective cells found in the Hippocampal-Entorhinal system, or build your own more complex cell type.
• Build and train complex networks Build, train and analyse complex networks of cells, powered by data generated with RatInABox.

RatInABox is an open source project welcoming contributions. If you use RatInABox please cite the paper and consider giving this repository a star ☆. It contains three classes:

1. Environment📦: The environment/maze (or "box") that the agent lives in. 1- or 2-dimensional.
2. Agent 🐀: The agent (or "rat") moving around the Environment.
3. Neurons 🧠: A population of neurons with firing rates determined by the state (position and velocity) of the Agent. Make your own or use one of our premade cell types including:
   • PlaceCells
   • GridCells
   • BoundaryVectorCells (egocentric or allocentric)
   • VelocityCells
   • SpeedCells
   • HeadDirectionCells
   • FeedForwardLayer (a generic class analagous to a feedforward layer in a deep neural network)
   • ...

The top animation shows an example use case: an Agent randomly explores a 2D Environment with a wall. Three populations of Neurons (PlaceCells, GridCells, BoundaryVectorCells) fire according to the receptive fields shown. All data is saved into the history for downstream use. RatInABox is fully continuous is space; this means that position and neuronal firing rates are calculated rapidly online with float precision rather than pre-calculated over a discretised mesh. RatInABox is flexibly discretised in time; dt can be set by the user (defaulting to 10 ms) depending on requirements.

Key features

• Non-specific: Trajectories can be randomly generated, imported, or adaptively controlled making RatInABox a powerful engine for many tasks involving continuous motion (e.g. control theory or reinforcement learning).
• Biological: Simulate large populations of spatially and/or velocity modulated cell types. Neurons can be rate based or spiking. The random motion model is fitted to match real rodent motion.
• Flexible: Simulate environments in 1D or 2D with arbitrarily wall arrangements. Combine premade or bespoke Neurons classes into arbitrary deep networks (examples given).
• Fast: Simulating 1 minute of exploration in a 2D environment with 100 place cells (dt=10 ms) take just 2 seconds on a laptop (no GPU needed).
• Precise: No more prediscretised positions, tabular state spaces, or jerky movement policies. It's all continuous.
• Easy: Sensible default parameters mean you can have realisitic simulation data to work with in ~10 lines of code.
• Visual Plot or animate trajectories, firing rate timeseries', spike rasters, receptive fields, heat maps, velocity histograms...using the plotting functions (summarised here).

Get started

Many demos are provided. Reading through the example scripts (one simple and one extensive, duplicated at the bottom of the readme) these should be enough to get started. We also provide numerous interactive jupyter scripts as more in-depth case studies; for example one where RatInABox is used for reinforcement learning, another for neural decoding of position from firing rate. Jupyter scripts reproducing all figures in the paper and readme are also provided.

Requirements, Installing and Importing

Requirements are minimal (python3, numpy, scipy and matplotlib, listed in setup.cfg) and will be installed automatically.

Install the latest, stable version using pip at the command line with

$ pip install ratinabox

Alternatively, in particular if you would like to edit RatInABox code, install locally using

$ git clone --depth 1 https://github.com/TomGeorge1234/RatInABox.git
$ cd RatInABox
$ pip install -e .

n.b. the -e (--editable) handle means this install points directly to the cloned repository itself. Any changes made here will be reflected when you next import RatInABox into your code. If you want to run the demo jupyter scripts please replace the last call with pip install -e .[demos].

Import into your python project with

import ratinabox
from ratinabox.Environment import Environment
from ratinabox.Agent import Agent
from ratinabox.Neurons import PlaceCells, GridCells #...

Feature run-down

Here is a list of features loosely organised into three categories: those pertaining to (i) the Environment, (ii) the Agent and (iii) the Neurons. Specific details can be found in the paper, here.

(i) Environment features

Walls

Arbitrarily add walls to the environment to produce arbitrarily complex mazes:

Environment.add_wall([[x0,y0],[x1,y1]])

Here are some easy to make examples.

Boundary conditions

Boundary conditions can be "periodic" or "solid". Place cells and the motion of the Agent will respect these boundaries accordingly.

Env = Environment(
    params = {'boundary_conditions':'periodic'} #or 'solid' (default)
) 

1- or 2-dimensions

RatInABox supports 1- or 2-dimensional Environments. Almost all applicable features and plotting functions work in both. The following figure shows 1 minute of exploration of an Agent in a 1D environment with periodic boundary conditions spanned by 10 place cells.

Env = Environment(
    params = {'dimensionality':'1D'} #or '2D' (default)
) 

(ii) Agent features

Random motion model

Random motion is stochastic but smooth. The speed (and rotational speed, if in 2D) of an Agent take constrained random walks governed by Ornstein-Uhlenbeck processes. You can change the means, variance and coherence times of these processes to control the shape of the trajectory. Default parameters are fit to real rat locomotion data from Sargolini et al. (2006):

The default parameters can be changed to obtain different style trajectories. The following set of trajectories were generated by modifying the rotational speed parameter Agent.rotational_velocity_std:

Agent.speed_mean = 0.08 #m/s
Agent.speed_coherence_time = 0.7
Agent.rotation_velocity_std = 120 * np.pi/180 #radians 
Agent.rotational_velocity_coherence_time = 0.08

Importing trajectories

RatInABox supports importing external trajectory data (rather than using the in built random motion policy). Imported data can be of low temporal resolution. It will be smoothly upsampled using a cubic splines interpolation technique. We provide a 10 minute trajectory from the open-source data set of Sargolini et al. (2006) ready to import. In the following figure blue shows (low resolution) trajectory data imported into an Agent and purple shows the smoothly upsampled trajectory taken by the Agent during exploration.

Agent.import_trajectory(dataset='sargolini')
#or 
Agent.import_trajectory(times=array_of_times,
                        positions=array_of_positions)

Policy control

By default the movement policy is an random and uncontrolled (e.g. displayed above). It is possible, however, to manually pass a "drift_velocity" to the Agent on each Agent.update() step. This 'closes the loop' allowing, for example, Actor-Critic systems to control the Agent policy. As a demonstration that this method can be used to control the agent's movement we set a radial drift velocity to encourage circular motion. We also use RatInABox to perform a simple model-free RL task and find a reward hidden behind a wall (the full script is given as an example script here)

Agent.update(drift_velocity=drift_velocity)

Wall repelling

Under the random motion policy, walls in the environment mildly "repel" the agent. Coupled with the finite turning speed this replicates an effect (known as thigmotaxis, sometimes linked to anxiety) where the agent is biased to over-explore near walls and corners (as shown in these heatmaps) matching real rodent behaviour. It can be turned up or down with the thigmotaxis parameter.

Αgent.thigmotaxis = 0.8 #1 = high thigmotaxis (left plot), 0 = low (right)

(iii) Neurons features

Multiple cell types:

We provide a list of premade Neurons subclasses. These include:

• PlaceCells
• GridCells
• BoundaryVectorCells (can be egocentric or allocentric)
• VelocityCells
• SpeedCells
• HeadDirectionCells
• FeedForwardLayer - calculates activated weighted sum of inputs from a provide list of input Neurons layers.

This last class, FeedForwardLayer deserves special mention. Instead of its firing rate being determined explicitly by the state of the Agent it summates synaptic inputs from a provided list of input layers (which can be any Neurons subclass). This layer is the building block for how more complex networks can be studied using RatInABox.

Place cell models:

Place cells come in multiple types (given by params['description']), or it would be easy to write your own:

• "gaussian": normal gaussian place cell
• "gaussian_threshold": gaussian thresholded at 1 sigma
• "diff_of_gaussians": gaussian(sigma) - gaussian(1.5 sigma)
• "top_hat": circular receptive field, max firing rate within, min firing rate otherwise
• "one_hot": the closest palce cell to any given location is established. This and only this cell fires.

This last place cell type, "one_hot" is particularly useful as it essentially rediscretises space and tabularises the state space (gridworld again). This can be used to contrast and compare learning algorithms acting over continuous vs discrete state spaces. This figure compares the 5 place cell models for population of 9 place cells (top left shows centres of place cells, and in all cases the "widths" parameters is set to 0.2 m, or irrelevant in the case of "one_hot"s)

These place cells (with the exception of "one_hot"s) can all be made to phase precess by instead initialising them with the PhasePrecessingPlaceCells() class currently residing in the contribs folder. This figure shows example output data.

Geometry of PlaceCells

Choose how you want PlaceCells to interact with walls in the Environment. We provide three types of geometries.

Spiking

All neurons are rate based. However, at each update spikes are sampled as though neurons were Poisson neurons. These are stored in Neurons.history['spikes']. The max and min firing rates can be set with Neurons.max_fr and Neurons.min_fr.

Neurons.plot_ratemap(spikes=True)

Rate maps

PlaceCells, GridCells and allocentric BoundaryVectorCells (among others) have firing rates which depend exclusively on the position of the agent. These rate maps can be displayed by querying their firing rate at an array of positions spanning the environment, then plotting. This process is done for you using the function Neurons.plot_rate_map().

More generally, however, cells firing is not only determined by position but potentially other factors (e.g. velocity or historical effects if the layer is part of a recurrent network). In these cases the above method of plotting rate maps will fail. A more robust way to display the receptive field is to plot a heatmap of the positions of the Agent has visited where each positions contribution to a bin is weighted by the firing rate observed at that position. Over time, as coverage become complete, the firing fields become visible.

Neurons.plot_rate_map() #attempted to plot "ground truth" rate map 
Neurons.plot_rate_map(method="history") #plots rate map by firing-rate-weighted position heatmap

More complex Neuron types and networks of Neurons

We encourage users to create their own subclasses of Neurons. This is easy to do, see comments in the Neurons class within the code for explanation. By forming these classes from the parent Neurons class, the plotting and analysis features described above remain available to these bespoke Neuron types. Additionally we provide a Neurons subclass called FeedForwardLayer. This neuron sums inputs from any proived list of other Neurons classes and can be used as the building block for constructing complex multilayer networks of Neurons, as we do here and here.

Example Scripts

In the folder called demos we provide numerous script and demos which will help when learning RatInABox. In approximate order of complexity, these include:

• simple_example.ipynb: a very simple tutorial for importing RiaB, initialising an Environment, Agent and some PlaceCells, running a brief simulation and outputting some data. Code copied here for convenience.

import ratinabox #IMPORT 
from ratinabox.Environment import Environment
from ratinabox.Agent import Agent
from ratinabox.Neurons import *
#INITIALISE CLASSES
Env = Environment() 
Ag = Agent(Env)
PCs = PlaceCells(Ag)
#EXPLORE
for i in range(int(20/Ag.dt)): 
    Ag.update()
    PCs.update()
#ANALYSE/PLOT
print(Ag.history['pos'][:10]) 
print(PCs.history['firingrate'][:10])
fig, ax = Ag.plot_trajectory()
fig, ax = PCs.plot_rate_timeseries()

• extensive_example.ipynb: a more involved tutorial. More complex enivornment, more complex cell types and more complex plots are used.
• list_of_plotting_functions.md: All the types of plots available for are listed and explained.
• readme_figures.ipynb: (Almost) all plots/animations shown in the root readme are produced from this script (plus some minor formatting done afterwards in powerpoint).
• paper_figures.ipynb: (Almost) all plots/animations shown in the paper are produced from this script (plus some major formatting done afterwards in powerpoint).
• decoding_position_example.ipynb: Postion is decoded from neural data generated with RatInABox. Place cells, grid cell and boundary vector cells are compared.
• reinforcement_learning_example.ipynb: RatInABox is use to construct, train and visualise a small two-layer network capable of model free reinforcement learning in order to find a reward hidden behind a wall.
• path_integration_example.ipynb: RatInABox is use to construct, train and visualise a large multi-layer network capable of learning a "ring attractor" capable of path integrating a position estimate using only velocity inputs.

Contribute

RatInABox is an open source project, and we actively encourage community contributions. These can take various forms, such as new movement policies, new cells types, new plotting functions, new geometries, bug fixes, documentation, citations of relevant work, or additional experiment notebooks. If there is a small contribution you would like to make, please feel free to open a pull request, and we can review it. For bugs and bug fixes please raise an issue. If you would like to add a new Neurons class please pull request it into the contribs directory. If there is a larger contribution you are considering please contact the correponding author at [e-mail].

Cite

If you use RatInABox in your research or educational material, please cite the work as follows: Bibtex:

@article{ratinabox2022,
	doi = {10.1101/2022.08.10.503541},
	url = {https://doi.org/10.1101%2F2022.08.10.503541},
	year = 2022,
	month = {aug},
	publisher = {Cold Spring Harbor Laboratory},
	author = {Tom M George and William de Cothi and Claudia Clopath and Kimberly Stachenfeld and Caswell Barry},
	title = {{RatInABox}: A toolkit for modelling locomotion and neuronal activity in continuous environments}
}

Formatted:

Tom M George, William de Cothi, Claudia Clopath, Kimberly Stachenfeld, Caswell Barry. "RatInABox: A toolkit for modelling locomotion and neuronal activity in continuous environments" (2022).

The research paper corresponding to the above citation can be found here.