November 2, 2013

Topological analysis of population activity in visual cortex

Singh, G., Memoli, F., Ishkhanov, T., Sapiro, G., Carlsson, G., & Ringach, D. L. (2008). Topological analysis of population activity in visual cortex. Journal of Vision, 8(8):11, 1–18,, doi:10.1167/8.8.11

From sparsely sampled data, we can attempt to estimate some of topological structure of the data.

Toplogical structure is here represented by Betti numbers. The paper explains this best:

Consider a world where objects are made of elastic rubber. Two objects are considered equivalent if they can be deformed into each other without tearing the material. If such a transformation between X and Y exists, we say they are topologically equivalent……it is evident that a possible reason for two objects not to be equivalent is that they differ in the number of holes. Thus, simply counting holes can provide a signature for the object at hand. Holes can exist in different dimensions. A one-dimensional hole is exposed when a one-dimensional loop (a closed curve) on the object cannot be deformed into a single point without tearing the loop. If two such loops can be deformed into one another they define the same hole, which should be counted only once. Analogous definitions can be invoked in higher dimensions. For example, a two-dimensional hole is revealed when a closed two-dimensional oriented surface on the object cannot be deformed into a single point.

This notion of counting holes of different dimensions is formalized by the definition of Betti numbers. The Betti numbers of an object X can be arranged in a sequence, b ( X )=( b 0 , b 1 , b 2 , I ), where b 0 represents the number of connected components, b 1 represents the number of one- dimensional holes, b 2 the number of two-dimensional holes, and so forth. An important property of Betti sequences is that if two objects are topologically equiv- alent (they can be deformed into each other) they share the same Betti sequence. One must note, as we will shortly illustrate, that the reverse is not always true: two objects can be different but have the same Betti sequence.

A technique is presented for estimating the Betti numbers of sampled data using “Rips complexes” and “barcodes”. To put this technique to use on neural data, the spiking of 5 cells (mostly “complex cells in the superficial layers”) with high spontaineous rate in V1 in Macaques were recorded from. The spikes were binned and a point cloud in 5D was constructed (so i think the coordinates of the point cloud representing the spike rate in each of the 5 dimensions).

This was done in two experimental conditions, when a stimulus was being presented, and when the eyes were occluded. In both cases, the topological structure varied between a circle and a sphere, although the circle structure was found with higher probability in the stimulus condition. The authors present a model of circular structure generated “if cortical activity is dominated by neuronal responses to stimulus orientation”, and a model of toroidal structure generated “A toroidal representation may arise from a neuronal population responding to two circular variables, such as orientation and color hue”. Note that a torus wasn’t actually observed in the data; a circle and a sphere was. In the conclusions the authors speculate what could have caused the sphere.

The authors conclude that the topology of spiking patterns for “both the data for spontaneous and driven conditions have similar topological structures, with the signatures of the circle and the sphere dominating the results”.

READ MORE: Cortex, Data analysis

April 10, 2013

Technique named ‘clarity’ makes chunks of dead brain transparent, allowing fluorescent labeling

This technique takes a dead brain and permeates it with a transparent hydrogel matrix to keep proteins and nucleic acids in place. Then it removes the lipids. I guess the lipids are all that makes the brain opaque. At this point the brain is transparent but maintains its original structure so you can still label the proteins and nucleic acids.

April 2, 2013

Neuroscience as a new national priority

President Obama: “Now, it’s time to get to work.”

NYT article:


March 3, 2013

Limited mediated telepathy

A rat was implanted with a 32-unit microelectrode cortical array in either M1 or S1. The rat was then trained to choose between two alternatives based on external stimuli.

Meanwhile, another rat was implanted with 6 stimulating electrodes in the same area as the first rat. It was trained to choose between the same two alternatives based on a stimulation pattern conveyed via the electrodes.

Then the signals recorded from the first rat’s brain were processed ald sent into the second rat’s brain. Both rats were trained together and both were rewarded when both made the right choice. The second rat learned to make the same choice as the first rat 60% of the time.

Miguel Pais-Vieira, Mikhail Lebedev, Carolina Kunicki, Jing Wang, Miguel A. L. Nicolelis. A Brain-to-Brain Interface for Real-Time Sharing of Sensorimotor Information. Scientific Reports 3, Article number: 1319. Received 20 December 2012.

READ MORE: Neural prosthetics

January 28, 2013

A subpopulation of nociceptors specifically linked to itch

Excerpt from the abstract: “We genetically labeled and manipulated MrgprA3+ neurons in the dorsal root ganglion (DRG) and found that they exclusively innervated the epidermis of the skin and responded to multiple pruritogens. Ablation of MrgprA3+ neurons led to substantial reductions in scratching evoked by multiple pruritogens and occurring spontaneously under chronic itch conditions, whereas pain sensitivity remained intact.”

READ MORE: Medicine

December 6, 2011

Hippocampus may still have a role in recalling old memories

Paraphrasing/adding to the article abstract: prevailing theory suggests that long-term memories are encoded via a two-phase process requiring temporary involvement of the hippocampus followed by permanent storage in the neocortex. However this group found that, even weeks later, after the memories are supposed to be independent of the hippocampus, they could disrupt recall by briefly suppressing hippocampal CA1. The suppression must be brief; if they suppress CA1 for a long time recall works again. This suggests that, long after memory formation, the memory is not primarily stored in the hippocampus, but the hippocampus is still somehow involved in recall. The research also implicates anterior cingulate cortex in recall. Abstract after the break.

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READ MORE: Memory systems

September 27, 2011

Scientists use MRI to reveal the movies in our mind

Scientists use brain imaging to reveal the movies in our mind.

June 17, 2011

Hippocampal CA1 prosthesis affects memory

Berger, Hampson, Song, Goonawardena, Marmarelis, and Deadwyler created a system for recording from and stimulating up to 32 neurons at once. The system learned a model to predict firing of some hippocampal CA1 neurons given some inputs from CA3, and could be “played back” later.

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READ MORE: Memory systems

May 27, 2011

Multisensory homunculi align

Read on for a talk abstract describing aligned visual and tactile homunculi in parietal cortex.

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Neurons with similar tuning more likely to be connected

From the abstract: … we determine synaptic connectivity between nearby layer 2/3 pyramidal neurons in vitro, the response properties of which were first characterized in mouse visual cortex in vivo. We found that connection probability was related to the similarity of visually driven neuronal activity. Neurons with the same preference for oriented stimuli connected at twice the rate of neurons with orthogonal orientation preferences. Neurons responding similarly to naturalistic stimuli formed connections at much higher rates than those with uncorrelated responses. Bidirectional synaptic connections were found more frequently between neuronal pairs with strongly correlated visual responses….

Ho Ko, Sonja B. Hofer, Bruno Pichler, Katherine A. Buchanan, P. Jesper Sjöström, Thomas D. Mrsic-Flogel. Functional specificity of local synaptic connections in neocortical networks. Nature. 2011 May 5;473(7345):87-91. Epub 2011 Apr 10.

READ MORE: Connectivity