Laboratory of Computing Biological Networks - retina

Information in the Retina and Experiments on Photon Counting

Kevin Sean Chen — Fri, 24 Jul 2015 16:58:17 +0000

There are mainly two parts in my presentation this time, results and analysis for the omitted stimulus response (OSR) experiment with spatial stimuli and some preliminary tests for photon counting in retina.

Last time, I talked about a hypothesized simple columnar organization that produces OSR in the retina. We may investigate the circuits by providing light stimuli with spatial patterns. Uniform, checkerboard, and random distributed pixels were used as the periodic stimulus. Fixing the number of flashes, period, and the average brightness, we see that OSR can only be generated under uniform, checkerboard or fixed random pixels (that are unchanged within a trial), but not in the anti-checkerboard or random pixel stimuli (that changes in every flashes). This implies that there may be specific spatial units to produce OSR. Further investigation is needed to identify the size and properties of these units.

In addition, I calculated spatial correlation and temporal information from the spike trains in previous experiments. For spatial correlation, we find that the correlated distance is longer under uniform stimuli than random flickers or checkerboard. Interestingly, those producing OSR seem to also have shorter correlation distance than those that simply response to each light flashes. For temporal information, my extrapolation results seem to provide less entropy rate comparing to the previous researches. I might find another method that fits our experiment better to calculate temporal information. Lastly, I’ve been reading articles focusing on the strong inhibitions in the retina. The inhibitory signal may not only play an important role in the anti-Hebbian model but also help encoding information through silencing neighbor neurons. Since we've been recently discussing the strong inhibition right after OSR, I'm also interested in how OSR affects the synergitic codes in retina.

For photon counting on the retina, I briefly went through some classic experiments showing the single photon sensitivity and detection of photon statistics in photoreceptor cells. Most researches focus on the gain control and regulation of threshold in the retina under dim light. In the future, we hope to calculate the correlation between spikes from ganglion cells, which really send information to the brain, to investigate whether photon information could still preserve after processing through the retinal circuits.

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retina

OSR

Information

Photon Counting

group meeting

Progress, future works on OSR, and some discussions on retina wave

Kevin Sean Chen — Sat, 06 Jun 2015 06:49:05 +0000

Some results from our experiments on OSR were shown in the slides. By holding the last state after terminating the periodic stimulus in an inverted manner (differ from the originally adapted brightness), OSR could be eliminated or shifted significantly in the latency. We’ll try to repeat the experiments a few more times, since such designed stimuli would tell us more about how ON and OFF pathways in the retina interact to produce OSR.

In the hypothetical circuit in the retina to perform predictive coding as observed in the experiments, I think gap junctions might play an important role to also modulate the activity in space. Furthermore, I show the raw data before passing the filter or detecting spikes. We can guess that a strong, synchronized inhibition is generated when OSR occurs. To sum up, I plan to perform some spatial and temporal analysis according to some references from a group also working on frog retina. Also, flashing bars or checkerboards to test the affects on OSR may also be a good idea to investigate the mechanisms for dynamical predictive coding and analyze the circuit in retina.

In the second part, I reported an article about the segregation and desynchronization of ON and OFF pathways during a certain stage in retina waves. The organization of ON and OFF paths may affect the connection in LGN and also some important orientation selectivity in V1 cortex. In result, ON bipolar sends lateral inhibition to OFF bipolar cells through inhibitory neurons like amacrine. Also, controlling the reuptake of glutamate by Mulller cells in the retina also affects the temporal precision for retina waves. Last but not least, most of theses cells are connected through gap junction, which also participates in strong inspatial synchrony. Since we're now able to recieve signals from the embryonic retina, we're optimistic to repeat some experiments in the refernce and try to stimulate it with different dynamical light patterns.

Tags:

retina

Omitted Stimulus Response

Predictive Coding

Retina Wave

group meeting

Progress report on EGTA and OSR measurement in retina

Kevin Sean Chen — Sat, 02 May 2015 07:01:46 +0000

During the last two months, we started adding EGTA, a calcium chelator in the buffer and observed change in OSR. Surprisingly, period doubling occurred at some specific concentration, and didn’t abolish OSR. We think that EGTA affects the time scale in the whole retina activity.

Following up, we designed light stimuli with two periods and also produced activity similar to period doubling, then measured the latency of OSR. In fact, the latency seems to be highly dependent to the last pulse. We can control the latency through the brightness of the last pulse. This may be a useful method for our future work, to do real-time feedbacks on retina for latency control.

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A hypothetical rivalry in retina and some spike sorting progress

Kevin Sean Chen — Mon, 05 Jan 2015 17:28:22 +0000

As observed in my experiments, "achromatic" receptive fields may react similarly to blue or green light stimuli, which are the two observable colors in bullfrogs. However, under intermeshed blue and green light stimulus, we constantly (such experiment had been repeated for more than five times) see the activity of recorded ganglion cells synchronize to only one color. I suspect that the retina randomly "follow" a color, since the same retina could produce activity following blue or green light under a same stimulus, and uninfluenced by the starting color.

Turning to a theoretical view, I want to build an analogy from “binocular rivalry”, a well-known phenomenon in psychophysics. I borrowed a simple model for binocular rivalry from a reference. By tuning the time scale and increasing the mutual inhibition strength, the activities of two pathways show similar patterns from the experiment. Therefore, I’d like to claim that maybe such rivalry observed in the retina is due to simple inhibition between two parallel dichromatic processes, and this relation might even contribute to monocular rivalry observed in psychophysical experiments (as shown in the figure).

In Addition, I’m trying to perform spike sorting recently. I’m now able to sort different cell types by Offline Sorter, plot the spike trigger average and raster plots for each cells with Matlab, and also perform some simple clustering (However, I'm still looking for the criteria and methods to define different waveforms. There's a reference dicussing about it). In the future, I hope to map the physical positions back to where the cell locates on the MEA, and we’re also willing to calculate the receptive fields for further experiments on the interesting spatial dynamics in retina.

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