OpenScope visual loop:

A temporary repository for the OpenScope visual loop project

Installation

Dependencies:

• Windows OS (see Camstim package)
• python 2.7
• psychopy 1.82.01
• camstim 0.2.4
• matplotlib 2.2.3

Installation with Anaconda or Miniconda:

1. Navigate to repository and install conda environment:
   conda env create -f environment.yml

2. Activate the environment:
   conda activate allen_stimulus

3. Install the AIBS camstim package in the environment:
   pip install camstim/.

4. Install matplotlib library:
   conda install matplotlib

5. Download required video clips from movie_clips.zip and extract into the data directory.

Input files

The software requires two sets of input files. There should be a set of text files present under data/stimulus_orderings that indicate the display order of video clips for different phases of the experiment.

In addition, there should be a set of video clips (stored as raw .npy files).
These clips must be downloaded and extracted into the data folder from full_movies.zip and stored in the path data/full_movies.

For debugging purposes please download shortened versions of the movie clips from short_movies.zip and extracted into the data folder and store them in the path data/short_movies.

Running the scripts

1. Activate the environment:
   conda activate allen_stimulus

2. Run the stimulus_loop.py script (for group A input 0 and for group B input 1):
   python stimulus_loop.py 0

Debugging mode

To run the script stimulus_loop.py in debugging mode, comment out line 50 and uncomment line 57.
This will change the path of the movie clips from their full length version (i.e., 30 sec) to their shortened version (5 sec) with helpful labels.

Stimulus design

The experiment consists of two phases in which different sets of 30 sec long natural movies will be presented:

• Phase 1 consists of two natural movies (i.e., movie01 and movie02) and a constant gray screen (i.e., movie00).
• Phase 2 consists of 50 natural movies (i.e., movie03-movie52) and a constant gray screen (i.e., movie00).

Animals are assigned into two groups (A and B), each presented with the movies in different order.
In both groups, a total of 230 movies will be presented for a total time of 115 min:

1. For group A:

   • Phase 1:

     • 50 presentations of movie01 (25 min)
     • 10 presentations of movie00 (5 min)
     • 50 alternations between movie01 and movie02 (25 min)
     • 10 presentations of movie00 (5 min)

   • Phase 2:

     • 20 presentations of movie03 (10 min)
     • 10 presentations of movie00 (5 min)
     • 50 sequential presentations of movie03 to movie52 (25 min)
     • 10 presentations of movie00 (5 min)
     • 20 alternations between movie03 and movie52 (10 min)

2. For group B:

   • Phase 1:

     • 50 alternations between movie01 and movie02 (25 min)
     • 10 presentations of movie00 (5 min)
     • 50 presentations of movie01 (25 min)
     • 10 presentations of movie00 (5 min)

   • Phase 2:

     • 20 presentations of movie03 (10 min)
     • 10 presentations of movie00 (5 min)
     • 50 presentations of movie52 (25 min)
     • 10 presentations of movie00 (5 min)
     • 20 alternations between movie03 and movie52 (10 min)