19 posts · 18,250 views
Discussions on computational neuroscience, journal club, hot software and hardware, resources, Matlab, Python and C code
Patrick Mineault
19 posts
Sort by: Latest Post, Most Popular
View by: Condensed, Full
- January 24, 2013
- 06:00 PM
- 185 views
Category representation in the brain
by Patrick Mineault in xcorr
You can solve most problems in life by buying more computers – or grad students, or microscopes, or lasers for that matter. Some of Jack Gallant’s lab recent efforts in fMRI analysis are a good example of this approach. They published an interesting paper in Neuron last month about the representation of categories in cortex.
Objects can be classified by humans in thousands of different categories. How are those categories represented in cortex? How would you even try to locate whe........ Read more »
Huth, A., Nishimoto, S., Vu, A., & Gallant, J. (2012) A Continuous Semantic Space Describes the Representation of Thousands of Object and Action Categories across the Human Brain. Neuron, 76(6), 1210-1224. DOI: 10.1016/j.neuron.2012.10.014
- May 30, 2012
- 03:35 AM
- 483 views
Modifying body representation through vision and vice versa
by Patrick Mineault in xcorr
There’s a few interesting multi-modal illusions involving vision and another sense. Proprioception, the ability to sense the position of one’s body parts, is one sense that gets a bad rep; it’s not even included in the classic 5 senses. Yet it’s certainly quite important, and people that lose proprioception have difficulty functioning at first, a [...]... Read more »
Carlson, T., Alvarez, G., Wu, D., & Verstraten, F. (2010) Rapid Assimilation of External Objects Into the Body Schema. Psychological Science, 21(7), 1000-1005. DOI: 10.1177/0956797610371962
- May 24, 2012
- 05:36 PM
- 596 views
Hearing radio frequencies
by Patrick Mineault in xcorr
I was reading the Wikipedia article on tinnitus, and came across this pearl of a sentence: A common and often misdiagnosed condition that mimics tinnitus is Radio Frequency (RF) Hearing in which subjects have been tested and found to hear high-pitched transmission frequencies that sound similar to tinnitus. Hmm, what? Yes, humans, under special circumstances, [...]... Read more »
Elder, J., & Chou, C. (2003) Auditory response to pulsed radiofrequency energy. Bioelectromagnetics, 24(S6). DOI: 10.1002/bem.10163
- May 15, 2012
- 10:04 PM
- 542 views
Modeling the Spatial Reach of LFP
by Patrick Mineault in xcorr
As regular readers will know, I’ve been intrigued by the nature of local field potential for some time. There’s a recent paper in Neuron by Lindén et al. that uses a modeling approach to explain the spatial reach of the LFP. This is a subject of some controversy; the spatial reach of the LFP has [...]... Read more »
Lindén H, Tetzlaff T, Potjans TC, Pettersen KH, Grün S, Diesmann M, & Einevoll GT. (2011) Modeling the spatial reach of the LFP. Neuron, 72(5), 859-72. PMID: 22153380
- May 1, 2012
- 02:31 PM
- 667 views
Is beer the answer?
by Patrick Mineault in xcorr
Well-meaning friends and family members may suggest that you have a couple of drinks after living through a stressful event. A friend of mine had a bike accident recently that sent her over a car door and miraculously left her with only a few bruises. Having a couple of drinks immediately after this will of [...]... Read more »
Maes M, Delmeire L, Mylle J, & Altamura C. (2001) Risk and preventive factors of post-traumatic stress disorder (PTSD): alcohol consumption and intoxication prior to a traumatic event diminishes the relative risk to develop PTSD in response to that trauma. Journal of affective disorders, 63(1-3), 113-21. PMID: 11246087
- April 23, 2012
- 05:20 PM
- 804 views
A presentation on mouse vision
by Patrick Mineault in xcorr
We had a lab meeting on Thursday, and it was my turn to present. Since I’m waiting for data to come through, I didn’t have original research to present, so I did a presentation on mouse vision, which I’ve been reading a lot about recently. I recorded the narration, and if you have Powerpoint, you [...]... Read more »
Wang, Q., Sporns, O., & Burkhalter, A. (2012) Network Analysis of Corticocortical Connections Reveals Ventral and Dorsal Processing Streams in Mouse Visual Cortex. Journal of Neuroscience, 32(13), 4386-4399. DOI: 10.1523/JNEUROSCI.6063-11.2012
Wang, Q., Gao, E., & Burkhalter, A. (2011) Gateways of Ventral and Dorsal Streams in Mouse Visual Cortex. Journal of Neuroscience, 31(5), 1905-1918. DOI: 10.1523/JNEUROSCI.3488-10.2011
Smith SL, & Häusser M. (2010) Parallel processing of visual space by neighboring neurons in mouse visual cortex. Nature neuroscience, 13(9), 1144-9. PMID: 20711183
Kerlin, A., Andermann, M., Berezovskii, V., & Reid, R. (2010) Broadly Tuned Response Properties of Diverse Inhibitory Neuron Subtypes in Mouse Visual Cortex. Neuron, 67(5), 858-871. DOI: 10.1016/j.neuron.2010.08.002
Kätzel, D., Zemelman, B., Buetfering, C., Wölfel, M., & Miesenböck, G. (2010) The columnar and laminar organization of inhibitory connections to neocortical excitatory cells. Nature Neuroscience, 14(1), 100-107. DOI: 10.1038/nn.2687
- April 8, 2012
- 09:44 PM
- 821 views
Connectomics in the retina
by Patrick Mineault in xcorr
Connectomics and some of its promises made news last week when Sebastian Seung and Tony Movshon went head to head in a debate broadcast by Radiolab (archived here). I didn’t watch the webcast, but I wanted to point out a quite fascinating recent study by Briggman, Helmstaedter and Denk (2011) that shows some of the [...]... Read more »
Briggman KL, Helmstaedter M, & Denk W. (2011) Wiring specificity in the direction-selectivity circuit of the retina. Nature, 471(7337), 183-8. PMID: 21390125
Helmstaedter, M., Briggman, K., & Denk, W. (2011) High-accuracy neurite reconstruction for high-throughput neuroanatomy. Nature Neuroscience, 14(8), 1081-1088. DOI: 10.1038/nn.2868
Demb, J. (2007) Cellular Mechanisms for Direction Selectivity in the Retina. Neuron, 55(2), 179-186. DOI: 10.1016/j.neuron.2007.07.001
- April 5, 2012
- 02:14 AM
- 832 views
Topography conquers all
by Patrick Mineault in xcorr
The eye faithfully maps visual space to different positions on the retina. This retinotopy is preserved as the signal is forwarded from retinal ganglion cells to the LGN, then to V1, and onwards. Cells which are physically adjacent on a retinotopic map have receptive fields corresponding to similar positions in space. More generally, properties like [...]... Read more »
Kerlin, A., Andermann, M., Berezovskii, V., & Reid, R. (2010) Broadly Tuned Response Properties of Diverse Inhibitory Neuron Subtypes in Mouse Visual Cortex. Neuron, 67(5), 858-871. DOI: 10.1016/j.neuron.2010.08.002
Kätzel, D., Zemelman, B., Buetfering, C., Wölfel, M., & Miesenböck, G. (2010) The columnar and laminar organization of inhibitory connections to neocortical excitatory cells. Nature Neuroscience, 14(1), 100-107. DOI: 10.1038/nn.2687
Motter, B. (2009) Central V4 Receptive Fields Are Scaled by the V1 Cortical Magnification and Correspond to a Constant-Sized Sampling of the V1 Surface. Journal of Neuroscience, 29(18), 5749-5757. DOI: 10.1523/JNEUROSCI.4496-08.2009
- March 31, 2012
- 11:51 PM
- 927 views
Big ideas: Focus on computation
by Patrick Mineault in xcorr
Matteo Carandini has an editorial in the latest issue of Nature Neuroscience arguing that we should focus energy on studying neural computation. In this context, neural computation is understood as an intermediate level of complexity between low-level neural circuits and high-level behavior. He argues that trying to go from physical descriptions of circuits to large-scale [...]... Read more »
Carandini, M. (2012) From circuits to behavior: a bridge too far?. Nature Neuroscience, 15(4), 507-509. DOI: 10.1038/nn.3043
Kouh M, & Poggio T. (2008) A canonical neural circuit for cortical nonlinear operations. Neural computation, 20(6), 1427-51. PMID: 18254695
- March 19, 2012
- 03:47 PM
- 980 views
Normalization as a canonical neural computation
by Patrick Mineault in xcorr
There’s an excellent review on normalization in the January 2012 edition of Nature Reviews Neuroscience by Carandini and Heeger. The theory and mathematics of normalization have stayed consistent since the seminal papers Heeger (1992) and Carandini and Heeger (1994). The response of a given neuron is divided by the summed output of a normalization pool, [...]... Read more »
Carandini, M., & Heeger, D. (2012) Normalization as a canonical neural computation. Nature Reviews Neuroscience. DOI: 10.1038/nrn3136
Heeger, D. (2009) Normalization of cell responses in cat striate cortex. Visual Neuroscience, 9(02), 181. DOI: 10.1017/S0952523800009640
Carandini, M., & Heeger, D. (1994) Summation and division by neurons in primate visual cortex. Science, 264(5163), 1333-1336. DOI: 10.1126/science.8191289
- March 3, 2012
- 07:46 PM
- 925 views
Spikes trigger LFP waves: the rebuttal
by Patrick Mineault in xcorr
Nauhaus, Busse, Carandini and Dario Ringach published an influential paper in 2009 with pretty convincing evidence that spikes trigger traveling waves of activity visible in LFPs; that these waves travel laterally; and because the dynamics of these waves change during stimulation compared to spontaneous activity, that stimulation modulates functional connectivity. This could imply that a [...]... Read more »
Nauhaus, I., Busse, L., Ringach, D., & Carandini, M. (2012) Robustness of Traveling Waves in Ongoing Activity of Visual Cortex. Journal of Neuroscience, 32(9), 3088-3094. DOI: 10.1523/JNEUROSCI.5827-11.2012
Ray S, & Maunsell JH. (2011) Network Rhythms Influence the Relationship between Spike-Triggered Local Field Potential and Functional Connectivity. Journal of Neuroscience, 31(35), 12674-82. PMID: 21880928
Nauhaus I, Busse L, Carandini M, & Ringach DL. (2009) Stimulus contrast modulates functional connectivity in visual cortex. Nature neuroscience, 12(1), 70-6. PMID: 19029885
- November 20, 2011
- 03:37 PM
- 1,071 views
What’s the maximal frame rate humans can perceive?
by Patrick Mineault in xcorr
Danny Kopping asked on my Twitter account what’s the maximal frame rate that humans can perceive. It’s a tricky question, mostly because it can be interpreted in different ways. Let’s break it down into these two scenarios: 1. At what frequency should a display (say a CRT) refresh so that it doesn’t appear to flicker [...]... Read more »
Hecht S, & Smith EL. (1936) Intermittent stimulation by light : VI. area and the relation between critical frequency and intensity. The Journal of general physiology, 19(6), 979-89. PMID: 19872977
Spekreijse H, van Norren D, & van den Berg TJ. (1971) Flicker responses in monkey lateral geniculate nucleus and human perception of flicker. Proceedings of the National Academy of Sciences of the United States of America, 68(11), 2802-5. PMID: 5001396
Veitch, J., & McColl, S. (1995) Modulation of fluorescent light: Flicker rate and light source effects on visual performance and visual comfort. Lighting Research and Technology, 27(4), 243-256. DOI: 10.1177/14771535950270040301
Ruck, P. (1961) Photoreceptor Cell Response and Flicker Fusion Frequency in the Compound Eye of the Fly, Lucilia sericata (Meigen). Biological Bulletin, 120(3), 375. DOI: 10.2307/1539540
M. RUCCI, J. D. VICTOR, A. CASILE, X. KUANG. (2011) Fixational eye movements enhance sensitivity to high spatial frequencies in the retina and LGN. SFN 2011. info:/
- September 24, 2011
- 05:52 PM
- 1,293 views
Decoding fMRI activity evoked by natural movies
by Patrick Mineault in xcorr
The Gallant lab have just published a new paper in Current Biology about decoding visual activity in fMRI evoked through natural movies. TryNerdy has a very high level overview of the paper. Here I’ more interested in the nitty gritty computational/statistical details. The idea is to train an encoding model using fMRI responses during natural [...]... Read more »
Shinji Nishimoto, An T. Vu, Thomas Naselaris, Yuval Benjamini, Bin Yu, & Jack L. Gallant. (2011) Reconstructing visual experiences from brain activity evoked by natural movies. Current Biology. info:/10.1016/j.cub.2011.08.031
- September 16, 2011
- 08:53 PM
- 1,320 views
How many pixels make an object? Like, 30
by Patrick Mineault in xcorr
There’s a neat paper on the psychophysics of scene and object recognition in super-low resolution scenarios in Visual Neuroscience by A. Torralba (2009). The author sought to answer a rather interesting question: what image resolution is needed to support scene and object recognition? He took images from databases and created several different versions of them, [...]... Read more »
Torralba A. (2009) How many pixels make an image?. Visual neuroscience, 26(1), 123-31. PMID: 19216820
- September 14, 2011
- 05:40 PM
- 1,392 views
Spikes trigger LFP waves – not so fast
by Patrick Mineault in xcorr
There’s been a lot of buzz at recent conferences around a controversial new paper in J. Neurosci. from Ray and Maunsell on LFP traveling waves. It’s a pretty direct, and rather convincing rebuttal of an influential Nature Neuroscience paper by Nauhaus et al. published a couple of years ago. Initial findings Nauhaus found what seemed [...]... Read more »
Ray S, & Maunsell JH. (2011) Network Rhythms Influence the Relationship between Spike-Triggered Local Field Potential and Functional Connectivity. Journal of Neuroscience, 31(35), 12674-82. PMID: 21880928
Nauhaus I, Busse L, Carandini M, & Ringach DL. (2009) Stimulus contrast modulates functional connectivity in visual cortex. Nature neuroscience, 12(1), 70-6. PMID: 19029885
- August 10, 2011
- 08:00 PM
- 1,124 views
Temporal precision in the LGN
by Patrick Mineault in xcorr
There’s a new paper just out in J Neurosci by Dan Butts et al. (2011) that offers some key insights into temporal precision in the lateral geniculate nucleus (LGN). The spike trains of LGN cells are remarkably regular; while a Poisson train has Fano factor (variance to mean ratio) of 1, and cortical neurons in [...]... Read more »
Butts DA, Weng C, Jin J, Alonso JM, & Paninski L. (2011) Temporal Precision in the Visual Pathway through the Interplay of Excitation and Stimulus-Driven Suppression. The Journal of neuroscience, 31(31), 11313-27. PMID: 21813691
Peter Dayan, & Larry Abbott. (2001) Theoretical Neuroscience. MIT Press. info:other/0262041995
Berry MJ 2nd, & Meister M. (1998) Refractoriness and neural precision. The Journal of neuroscience : the official journal of the Society for Neuroscience, 18(6), 2200-11. PMID: 9482804
Keat J, Reinagel P, Reid RC, & Meister M. (2001) Predicting every spike: a model for the responses of visual neurons. Neuron, 30(3), 803-17. PMID: 11430813
Butts DA, Weng C, Jin J, Yeh CI, Lesica NA, Alonso JM, & Stanley GB. (2007) Temporal precision in the neural code and the timescales of natural vision. Nature, 449(7158), 92-5. PMID: 17805296
- July 5, 2011
- 04:44 PM
- 1,573 views
Hexagonal orientation maps in V1
by Patrick Mineault in xcorr
Interesting paper from Se-Bum Paik and Dario Ringach in this month’s issue of Nature Neuroscience on the origins of the orientation map in V1. Dr. Ringach has been developing a model of V1 orientation selectivity for a number of years now, the statistical connectivity hypothesis, based on the idea that the retinotopic map in V1 [...]... Read more »
Paik SB, & Ringach DL. (2011) Retinal origin of orientation maps in visual cortex. Nature neuroscience, 14(7), 919-25. PMID: 21623365
Smith SL, & Smith IT. (2011) Life imitates op art. Nature neuroscience, 14(7), 803-4. PMID: 21709673
Ringach DL. (2004) Haphazard wiring of simple receptive fields and orientation columns in visual cortex. Journal of neurophysiology, 92(1), 468-76. PMID: 14999045
Das A, & Gilbert CD. (1997) Distortions of visuotopic map match orientation singularities in primary visual cortex. Nature, 387(6633), 594-8. PMID: 9177346
- June 15, 2011
- 08:47 PM
- 1,684 views
The far-reaching influence of sparse coding in V1
by Patrick Mineault in xcorr
Introduction Olshausen and Field (1996) made a big splash in visual neurophysiology and machine learning by offering an answer to a provocative question: Why are simple cell receptive fields (RFs) organized the way they are? After all, they could just as well be shaped like elongated sine waves, as in Fourier analysis, or they could [...]... Read more »
Olshausen, B., & Field, D. (1996) Emergence of simple-cell receptive field properties by learning a sparse code for natural images. Nature, 381(6583), 607-609. DOI: 10.1038/381607a0
Honglak Lee, Alexis Battle, Rajat Raina, & Andrew Y. Ng. (2007) Efficient Sparse Coding Algorithms. Advances in Neural Information Processing Systems, 801-808. info:/
Vinje WE, & Gallant JL. (2000) Sparse coding and decorrelation in primary visual cortex during natural vision. Science (New York, N.Y.), 287(5456), 1273-6. PMID: 10678835
Olshausen BA, & Field DJ. (1997) Sparse coding with an overcomplete basis set: a strategy employed by V1?. Vision research, 37(23), 3311-25. PMID: 9425546
Hale, E., Yin, W., & Zhang, Y. (2008) Fixed-Point Continuation for L1-Minimization: Methodology and Convergence. SIAM Journal on Optimization, 19(3), 1107. DOI: 10.1137/070698920
Pack CC, Livingstone MS, Duffy KR, & Born RT. (2003) End-stopping and the aperture problem: two-dimensional motion signals in macaque V1. Neuron, 39(4), 671-80. PMID: 12925280
- May 12, 2011
- 02:59 PM
- 1,031 views
LFPs above 50Hz: is it all garbage?
by Patrick Mineault in xcorr
There’s a recent paper by the Maunsell lab in PLoS Biology that examines the origins of local field potentials in the low-gamma (30-80Hz) and high-gamma ranges (> 80 Hz) ranges. The paper uses a clever experimental paradigm that allows one to dissociate LFPs and spike activity through the phenomenon of surround suppression. Basically, in surround [...]... Read more »
Ray S, & Maunsell JH. (2011) Different origins of gamma rhythm and high-gamma activity in macaque visual cortex. PLoS biology, 9(4). PMID: 21532743
Zanos TP, Mineault PJ, & Pack CC. (2011) Removal of spurious correlations between spikes and local field potentials. Journal of neurophysiology, 105(1), 474-86. PMID: 21068271
topics
join us!
Do you write about peer-reviewed research in your blog? Use ResearchBlogging.org to make it easy for your readers — and others from around the world — to find your serious posts about academic research.
If you don't have a blog, you can still use our site to learn about fascinating developments in cutting-edge research from around the world.
