Overview
This repository contains all raw data (spike times), and modelling code for the manuscript "Macaque ganglion cells responses to natural scenes: time, not space is what they really care about"
For further inquiries, don't hesitate to get in touch with us
Barry Lee blee@sunyopt.edu
Manuel Schottdorf mschottdorf@princeton.edu
Funding for the project is through HHS, NIH, and the National Eye Institute EY13110
Organization of the repository
The repository is organized into five folders:
\data\ contains the raw data of individual cells, organized into plain-text tables of spike-times.
\stimuli\ contains the visual stimuli, and details for calibration, such as gamma correction and gun spectra.
\retinatools\ contains the python-code of the model. It is used as a python-library in the following two folders:
\run_model\ Contains jupyter-notebooks to to run the model, and reproduce the model-figures from the paper. This can be run on any laptop without problems. It also contains a subset of the data, obtained by averaging across the 6 1min repeats, for measuring model performance.
\run_model_HPC\ Contains the code to run the RGC model for whole arrays of cells, and was used to compute the supplemental movie (REMOVE BRODY).
All code was tested on mac os 11 with Python 3, numpy, scipy and cv2.
Details of the data files.
Organization of spiking data
The time resolution on these data is 0.1 msec. 10 min files. These ASCII files are records of spike occurrence. Total spikes are given and then the video start time (an internal control; it varies from cell to cell). The spikes/5 sec column are a check on firing rates through the video. In 0 are the total spikes before the video starts; time period is variable. The following 120 bins are spike counts in subsequent 5 sec epochs. Finally, bin 121 is spike count following the live video termination before recording was switched off. The spike time list that follows is referred to the begin of the live video (and have been corrected for a slight difference in clock rate between video and data acquisition computers). 6x1min files Format is similar. The first 1 min of the 10 min video is repeated 6 times. There is a variable delay (blank frames) before the beginning of the first live video repeat. The each live repeat is preceded by 5 sec of blank frames, and there are ca. 5 sec of blank frames after termination before the next repeat starts. After completion of the 6 repeats there is a further period of maintained activity (column 7).
Cell List
| File name |
Cell Type |
Record Duration |
Cell Key |
| Lss01071.txt |
-M+L off |
10 min |
67#4 |
| Lss01078.txt |
MC off |
6x1min |
67#6 |
| Lss01181.txt |
MC off |
6x1min |
68#3 |
| Lss01221.txt |
MC on |
10 min |
68#10 |
Details of the stimulus videos
1) 1x10_256.mpg This is the 10 minute video. It begins with 751 blank frames (approximately equal energy white) followed by the 10 min live video (starting at frame 752, 90000 frames) followed by 750 blank frames. These frames were played at 150 frames/sec, 3 times acquisition rate. Timing pulses are provided on the audio channel beginning at the first frame of the video. They have a complex pattern, repeating every 5 sec. They were provided to ensure syncing with the data acquisition system that recorded spike trains.
2) 6x1_256.mpg. This is 1 min video. Structure as in 1x10min, except only 9000 frames.
3) Gamma correction. The r,g,b, values (0-256) from the mpeg decompression can be converted to intensity values by
red = 0.01451 + 0.9855*pow(1.0*I/256, 2.3122);
green = 0.005123 + 0.9949*pow(1.0*I/256, 2.2752);
blue = 0.02612 + 0.9739*pow(1.0*I/256, 2.2818);
where I is the bit value.
4) Gun spectra. The spectra measured for the 3 display guns are tabulated in GunSpectra.txt Based on the gun spectra and luminance estimates, the gun values were calibrated to deliver the same luminance. However, based on reverse correlation analysis on M cells, it was estimated that, relative to the red gun, the green gun luminance was overestimated by ca. 5% and the blue gun underestimated by ca. 20%.
Model details
A codel for primate retinal MC/PC/KC responses to natural scenes
