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# Overview
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-This repository contains all raw data and modelling code for the manuscript *"Macaque ganglion cells responses to natural scenes: time, not space is what they really care about"*
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+This repository contains all raw data and modelling code for the manuscript *"A quantitative description of macaque ganglion cell responses to natural scenes: the interplay of time and space"*
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-For further inquiries, don't hesitate to get in touch with us<br/>
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+For further inquiries, don't hesitate to get in touch with us:<br/>
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Barry Lee <blee@sunyopt.edu><br/>
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Manuel Schottdorf <mschottdorf@princeton.edu>
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-Funding for the project: HHS, NIH, and the National Eye Institute via EY13110
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+Funding for the project: Max-Planck Society, NIH and the National Eye Institute via 5R01EY013112, and a Boehringer Ingelheim Fonds PhD Fellowship.
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----
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The data and code is licensed under a [Creative Commons Attribution 4.0 International License (CC BY)](https://creativecommons.org/licenses/by/4.0/), which means that you can copy, redistribute, remix, transform and build upon the content for any purpose even commercially as long as you give appropriate credit and provide a link to the license.
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@@ -33,9 +33,9 @@ The repository is organized into five folders:
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## Organization of spiking data
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There are two types of files for the 6x1min and 10min records. Both contain ASCII records of spike occurrence, and some meta information. The time resolution on all data is 0.1 msec.
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-* 10 min files. 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).
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+* 10 min files: 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).
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-* 6 x 1min 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).
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+* 6 x 1min 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 video repeat 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).
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## Cell List
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@@ -94,37 +94,35 @@ There are two types of files for the 6x1min and 10min records. Both contain ASCI
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0. The gun spectra were measured from the display, and are saved as raw text in `/stimuli/`. They are consistent with the typical spectral output of the phosphors of a CRT display: 
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-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.
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+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 syncronization with the data acquisition system that recorded spike trains.
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-2. 6x1_256.mpg. This is 1 min video. Structure as in 1x10min, except only 9000 frames.
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+2. 6x1_256.mpg. This is a 1 min video. Structure as in 1x10min, except only 9000 frames.
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-3. Gamma correction. The r,g,b, values (0-256) from the mpeg decompression can be converted to intensity values using the following equations, where I is the r/g/b bit value:
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+3. Gamma correction. The r,g,b, values (0-255) from the mpeg decompression can be converted to intensity values using the following equations, where I is the r/g/b bit value:
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```
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red = 0.01451 + 0.9855*pow(1.0*I/256, 2.3122);
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green = 0.005123 + 0.9949*pow(1.0*I/256, 2.2752);
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blue = 0.02612 + 0.9739*pow(1.0*I/256, 2.2818);
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```
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-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%. The gamma-corrected intensities can be converted into l/m/s cone signals using the following equation:
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+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%. We therefore converged on the following equation to convert gamma-corrected intensities into l/m/s cone signals:
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```
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- lcone = 2.74*rgamma + 3.4*ggamma + 1.34*bgamma
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- mcone = 1.21*(1.06*rgamma + 3.58*ggamma + 2.07*bgamma)
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- scone = 0.212*rgamma + 8.28*ggamma + 285*bgamma
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+ lcone = 2.74*red + 3.4*green + 1.34*blue
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+ mcone = 1.21*(1.06*red + 3.58*green + 2.07*blue)
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+ scone = 0.212*red + 8.28*green + 285*blue
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```
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-5. These parameters were considered constant and not further optimized.
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+5. These equations and parameters were considered constant across cells, and not further optimized.
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# Model details
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1. The averaged 6 x 1 min responses were best for modeling, while the 10 min runs gave better results for the reverse correlation.
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-1. For rates, using filters employed in the previous paper (van Hateren et al.,
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-2002); 8-stage low pass filters were used with time constants of 2 msec for MC-cells
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-and 4 msec for PC- and S-cone cells.
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+1. For firing rates, we used filters employed in (van Hateren et al. 2002). More specifically, we used an 8-stage low pass filter with time constants of 2 msec for MC-cell and 4 msec for PC- and S-cone cells.
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-1. The model provides additional data files in /data with the averaged 6x 1min into firing rates. The format of these files is 2xT, where the first column is the cells activity, and the second column is an estimate of luminance. For modelling, we only use column 1.
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+1. The model provides additional data files in /data with the averaged 6 x 1 min responses converted into firing rates. The format of these files is 2xT, where the first column is the cells activity, and the second column is an estimate of luminance. For modelling, we only use column 1.
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-2. A codel for primate retinal MC/PC/KC responses to natural scenes, produces fits to the following cells:
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+1. Our model for primate retinal MC/PC/KC responses to natural scenes produces fits to the following cells. The column with correlation coefficients illustrates model respective model performance:
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| File name | Cell Type | corr. with model | Notes |
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|---------------|-----------------|-------------------|------------|
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@@ -145,8 +143,8 @@ and 4 msec for PC- and S-cone cells.
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| 299 | MC on | 0.826 | ok |
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| 302 | S on | 0.732 | ok |
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-Cellslist which is a summary of all video data. Some cells are noted as poor or lost. Yellow cells have been fully analysed. Red records were various controls Hans wanted, including repeats with ND filters before the eye to see what happens. I've not analyzed them. There are a number of cells in which there are 6 repeats of the 10 min runs, and others with fewer. Usually repeat reverse correlation plots and temporal IRs were very similar.
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-And in addition reproduces the pie charts.
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-We also provide one example for a PC Off cell, where the fit seems to work well. The model is identical to all PC fits.
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+1. We also provide code to reproduce the pie-charts
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+
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+1. And an example fit to a +L-M PC off cell (#225), with a fit of r~0.80. The model is identical to all PC cells, and the off response to luminance caused by the specific linear weights to M and L cones.
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