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[0] Is this the bionic man?Nature 442:7099, 109 (2006 Jul 13)[1] Hochberg LR, Serruya MD, Friehs GM, Mukand JA, Saleh M, Caplan AH, Branner A, Chen D, Penn RD, Donoghue JP, Neuronal ensemble control of prosthetic devices by a human with tetraplegia.Nature 442:7099, 164-71 (2006 Jul 13)[2] Santhanam G, Ryu SI, Yu BM, Afshar A, Shenoy KV, A high-performance brain-computer interface.Nature 442:7099, 195-8 (2006 Jul 13)[3] Shenoy KV, Meeker D, Cao S, Kureshi SA, Pesaran B, Buneo CA, Batista AP, Mitra PP, Burdick JW, Andersen RA, Neural prosthetic control signals from plan activity.Neuroreport 14:4, 591-6 (2003 Mar 24)

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ref: -2017 tags: GraphSAGE graph neural network GNN date: 07-16-2020 15:49 gmt revision:2 [1] [0] [head]

Inductive representation learning on large graphs

  • William L. Hamilton, Rex Ying, Jure Leskovec
  • Problem: given a graph where each node has a set of (possibly varied) attributes, create a 'embedding' vector at each node that describes both the node and the network that surrounds it.
  • To this point (2017) there were two ways of doing this -- through matrix factorization methods, and through graph convolutional networks.
    • The matrix factorization methods or spectral methods (similar to multi-dimensional scaling, where points are projected onto a plane to preserve a distance metric) are transductive : they work entirely within-data, and don't directly generalize to new data.
      • This is parsimonious in some sense, but doesn't work well in the real world, where datasets are constantly changing and frequently growing.
  • Their approach is similar to graph convolutional networks, where (I think) the convolution is indexed by node distances.
  • General idea: each node starts out with an embedding vector = its attribute or feature vector.
  • Then, all neighboring nodes are aggregated by sampling a fixed number of the nearest neighbors (fixed for computational reasons).
    • Aggregation can be mean aggregation, LSTM aggregation (on random permuations of the neighbor nodes), or MLP -> nonlinearity -> max-pooling. Pooling has the most wins, though all seem to work...
  • The aggregated vector is concatenated with the current node feature vector, and this is fed through a learned weighting matrix and nonlinearity to output the feature vector for the current pass.
  • Passes proceed from out-in... i think.
  • Algorithm is inspired by the Weisfeiler-Lehman Isomorphism Test, which updates neighbor counts per node to estimate if graphs are isomorphic. They do a similar thing here, only with vectors not scalars, and similarly take into account the local graph structure.
    • All the aggregator functions, and for course the nonlinearities and weighting matricies, are differentiable -- so the structure is trained in a supervised way with SGD.

This is a well-put together paper, with some proofs of convergence etc -- but it still feels only lightly tested. As with many of these papers, could benefit from a positive control, where the generating function is known & you can see how well the algorithm discovers it.

Otherwise, the structure / algorithm feels rather intuitive; surprising to me that it was not developed before the matrix factorization methods.

Worth comparing this to word2vec embeddings, where local words are used to predict the current word & the resulting vector in the neck-down of the NN is the representation.

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ref: -2017 tags: two photon holographic imaging Arch optogenetics GCaMP6 date: 09-12-2019 19:24 gmt revision:1 [0] [head]

PMID-28053310 Simultaneous high-speed imaging and optogenetic inhibition in the intact mouse brain.

  • Bovetti S1, Moretti C1, Zucca S1, Dal Maschio M1, Bonifazi P2,3, Fellin T1.
  • Image GCamp6 in either scanned mode (high resolution, slow) or holographically (SLM, redshirt 80x80 NeuroCCD, activate opsin Arch, simultaneously record juxtasomal action potentials.

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ref: -0 tags: 3D SHOT Alan Hillel Waller 2p photon holography date: 05-31-2019 22:19 gmt revision:4 [3] [2] [1] [0] [head]

PMID-29089483 Three-dimensional scanless holographic optogenetics with temporal focusing (3D-SHOT).

  • P├ęgard NC1,2, Mardinly AR1, Oldenburg IA1, Sridharan S1, Waller L2, Adesnik H3,4
  • Combines computer-generated holography and temporal focusing for single-shot (no scanning) two-photon photo-activation of opsins.
  • The beam intensity profile determines the dimensions of the custom temporal focusing pattern (CTFP), while phase, a previously unused degree of freedom, is engineered to make 3D holograph and temporal focusing compatible.
  • "To ensure good diffraction efficiency of all spectral components by the SLM, we used a lens Lc to apply a small spherical phase pattern. The focal length was adjusted so that each spectral component of the pulse spans across the short axis of the SLM in the Fourier domain".
    • That is, they spatially and temporally defocus the pulse to better fill the SLM. The short axis of the SLM in this case is Y, per supplementary figure 2.
  • The image of the diffraction grating determines the plane of temporal focusing (with lenses L1 and L2); there is a secondary geometric focus due to Lc behind the temporal plane, which serves as an aberration.
  • The diffraction grating causes the temporal pattern to scan to produce a semi-spherical stimulated area ('disc').
  • Rather than creating a custom 3D holographic shape for each neuron, the SLM is after the diffraction grating -- it imposes phase and space modulation to the CTFP, effectively convolving it with a holograph of a cloud of points & hence replicating at each point.

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ref: -2015 tags: conjugate light electron tomography mouse visual cortex fluorescent label UNC cryoembedding date: 03-11-2019 19:37 gmt revision:1 [0] [head]

PMID-25855189 Mapping Synapses by Conjugate Light-Electron Array Tomography

  • Use aligned interleaved immunofluorescence imaging follwed by array EM (FESEM). 70nm thick sections.
  • Of IHC, tissue must be dehydrated & embedded in a resin.
  • However, the dehydration disrupts cell membranes and ultrastructural details viewed via EM ...
  • Hence, EM microscopy uses osmium tetroxide to cross-link the lipids.
  • ... Yet that also disrupt / refolds the poteins, making IHC fail.
  • Solution is to dehydrate & embed at cryo temp, -70C, where the lipids do not dissolve. They used Lowicryl HM-20.
  • We show that cryoembedding provides markedly improved ultrastructure while still permitting multiplexed immunohistochemistry.

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ref: -0 tags: photoacoustic tomography mouse imaging q-switched laser date: 05-11-2017 05:23 gmt revision:1 [0] [head]

Single-impulse panoramic photoacoustic computed tomography of small-animal whole-body dynamics at high spatiotemporal resolution

  • Used Q-switched Nd:YAG and Ti:Sapphire lasers to illuminate mice axially (from the top, through a diffuser and conical lens), exciting the photoacuostic effect, from which they were able to image at 125um resolution a full slice of the mouse.
    • I'm surprised at their mode of illumination -- how do they eliminate the out-of-plane photoacoustic effect?
  • Images look low contrast, but structures, e.g. cortical vasculature, are visible.
  • Can image at the rep rate of the laser (50 Hz), and thereby record cardiac and pulmonary rhythms.
  • Suggest that the photoacoustic effect can be used to image brain activity, but spatial and temporal resolution are limited.

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ref: -0 tags: photoacoustic tomography mouse imaging q-switched laser date: 05-11-2017 05:21 gmt revision:0 [head]

Single-impulse panoramic photoacoustic computed tomography of small-animal whole-body dynamics at high spatiotemporal resolution

  • Used Q-switched Nd:YAG and Ti:Sapphire lasers to illuminate mice axially, exciting the photoacuostic effect, from which they were able to image at 125um resolution a full slice of the mouse.
  • Images look low contrast, but structures, e.g. cortical vasculature, are visible.
  • Can image at the rep rate of the laser (50 Hz), and thereby record cardiac and pulmonary rhythms.
  • Suggest that the photoacoustic effect can be used to image brain activity, but spatial and temporal resolution are limited.

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ref: -0 tags: graphene polyimide polymerization date: 01-22-2017 05:20 gmt revision:3 [2] [1] [0] [head]

Preparation and properties of graphene oxide/polyimide composite films with low dielectric constant and ultrahigh strength via in situpolymerization

  • The GO/PI composite films provide ultrahigh tensile strength (up to 844 MPa) and Young's modulus (20.5 GPa).
    • Almost 10x increase in tensile strength!
    • And even larger increase in modulus.
  • Also, you can reduce graphene / graphite oxide with an infrared laser: http://pubs.acs.org/doi/abs/10.1021/nn204200w

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ref: -0 tags: histology optical coherence tomography vasculature avoidance date: 01-29-2013 06:46 gmt revision:0 [head]

PMID-9766311 Optical coherence tomography for neurosurgical imaging of human intracortical melanoma.

  • Relevant for our interests: Subsurface cerebral vascular structures could be identified and were therefore avoided.
  • more broadly, could identify subsurface metastatic melanoma due to reflectance changes. nice.

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ref: -0 tags: optical coherence tomography neural recording squid voltage sensitive dyes review date: 12-23-2012 21:00 gmt revision:4 [3] [2] [1] [0] [head]

PMID-20844600 Detection of Neural Action Potentials Using Optical Coherence Tomography: Intensity and Phase Measurements with and without Dyes.

  • Optical methods of recording have been investigated since the 1940's:
    • During action potential (AP) propagation in neural tissue light scattering, absorption, birefringence, fluorescence, and volume changes have been reported (Cohen, 1973).
  • OCT is reflection-based, not transmission: illuminate and measure from the same side.
    • Here they use spectral domain OCT, where the mirror is not scanned; rather SD-OCT uses a spectrometer to record interference of back-scattered light from all depth points simultaneously (Fercher et al., 1995).
    • Use of a spectrometer allows imaging of an axial line within 10-50us, sufficient for imaging action potentials.
    • SD-OCT, due to some underlying mathematics which I can't quite grok atm, can resolve/annul common-mode phase noise for high temporal and Δphase\Delta phase measurement (high sensitivity).
      • This equates to "microsecond temporal resolution and sub-nanometer optical path length resolution".
  • OCT is generally (intially?) used for in-vivo imaging of retinas, in humans and other animals.
  • They present new data for depth-localization of neural activity in squid giant axons (SGA) stained with a voltage-sensitive near-infrared dye.
    • Note: averaged over 250 sweeps.
  • ΔPhase>>ΔIntensity\Delta Phase >> \Delta Intensity -- figure 4 in the paper.
  • Use of voltage-sensitive dyes improves the resolution of ΔI\Delta I , but not dramatically --
    • And Δphase\Delta phase is still a bit delayed.
    • Electrical recording is the control.
      • It will take significant technology development before optical methods exceed electrical methods...
  • Looks pretty preliminary. However, OCT can image 1-2mm deep in transparent tissue, which is exceptional.
  • Will have to read their explanation of OCT.
  • Used in a squid giant axon prep. 2010, wonder if anything new has been done (in vivo?).
  • Claim that progress is hampered by limited understanding of how these Δphase\Delta phase signals arise.

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ref: -0 tags: optical coherence tomography neural recording aplysia date: 12-23-2012 09:12 gmt revision:2 [1] [0] [head]

PMID-19654752 Detecting intrinsic scattering changes correlated to neuron action potentials using optical coherence imaging.

  • Aplysia, intrinsic imaging of scattering change following electrical stimulation.
    • Why did it take so long for them to get this paper out.. ?
  • Nicolelis first cited author.
  • Quality of recording not necessarily high.
  • quote: "Typical transverse resolutions in OCT (10-20um) are likely insufficient to identify smaller mamallian neurons that are often studied in neuroscience."
    • Solution: optical coherence microscopy (OCM), where a higher NA lens focuses the light to a smaller spot.
    • Expense: shorter depth-of-field.
  • Why does this work? "One mechanism of these optical signals is believed to be a realignment of charged membrane proteins in response to voltage change [6].
  • A delay of roughly 70ms was observed between the change in membrane voltage and the change in scattering intensity.
    • That's slow! Might be due to conduction velocity in Aplysia.
  • SNR of scattering measurement not too high -- the neurons are alive, afterall, and their normal biological processes cause scattering changes.
    • Killing the neurons with KCl dramatically decreased the variance of scattering, consistent with this hpothesis.
  • Birefringence: "Changes in the birefringence of nerves due to electrical activity have been shown to be an order of magnitude larger than scattering intensity changes" PMID-5649693

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ref: -0 tags: Moxon ceramic array electrode lithography date: 07-12-2012 23:05 gmt revision:3 [2] [1] [0] [head]

IEEE-1275580 (pdf) Ceramic-based Multisite Electrode array for Chronic Single-Neuron Recording

  • Their substrate is polished to 35-50um thick
  • patterned using standard lift-off lithographic techniques
  • four electrodes per shank
  • The ceramic is considerably stiffer than silicon (table) -- 372 Gpa vs. 190 Gpa.

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ref: -0 tags: Seymour thesis electrode lithography fabrication date: 02-05-2012 17:35 gmt revision:4 [3] [2] [1] [0] [head]

Advanced polymer-based microfabricated neural probes using biologically driven designs.

  • References {1109}
  • Thermal noise from 280 um^2 or 170 um^2 gold recording sites much higher than PEDOT coated sites.
  • Used an interdigitated contact-free probe for measuring insulation impedance change. Very smart!
    • Water molecules will diffuse 15 um / minute in parylene (Yasuda, Yu et. al 2010).
    • In the frequency range critical for neural recording and stimulation, 500-5k, impedance moculus decline was small.
    • 1 hr soak at 60C.
  • Chapter 3 details 60-day soak of Parylene-C + reactive parylene insulation performance testing.
    • Regular parylene seems to work perfectly fine, no better than the PPX heat-treated devices.
    • Heat treatment does improve quality -- 200C in a vacuum oven for 2 days. (Li, Rodger et al 2005)
      • However -- this increases the brittleness.

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ref: Wise-1970.07 tags: Wise MEA silicon gold lithography date: 01-03-2012 19:05 gmt revision:3 [2] [1] [0] [head]

IEEE-4502738 (pdf) An Integrated-Circuit Approach to Extracellular Microelectrodes

  • Used lithography techniques & to make SiO2 & Au electrodes.
  • 2um tips.
    • Back then, small tips were deemed good; nowadays, we want larger, lower-impedance tips (fad?)
  • Most previous work is glass insulated metal electrodes [1][2]
    • C. Guld, a glass-covered platinum microelectrode. {1014}
  • Probes cannot exceed more than 50um from the edge of the chip carrier without cracking, which limits how close one may get to a given cell.


Wise, Kensall D. and Angell, James B. and Starr, Arnold An Integrated-Circuit Approach to Extracellular Microelectrodes Biomedical Engineering, IEEE Transactions on BME-17 3 238 -247 (1970)

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ref: -0 tags: procreation babies commentary demography date: 01-03-2012 02:36 gmt revision:2 [1] [0] [head]

Demography: Babies make a comeback

  • The mathematical/ecomomic analysis of birth rates seems almost farcical to me without proper consideration of another vital point: culture. Yes, women may want to delay or renounce children to work, become more educated, travel, amass riches etc - but these are all strongly influenced by culture.
  • Another thought that they did not mention is that raising well-educated children is very expensive in developed countries - perhaps there is a tipping point where the parents have more than enough money to raise their kids to their satisfaction. (That said, I think this is less than likely given that parents are very competitive, at least in the US, with the education and support of their children).
  • Perhaps some understanding of why people in developed countries have children in the first place is warranted. I might recommend asking them to find out :-) Such information would help any purely economic theory.

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ref: -0 tags: processing javascript vector graphics web date: 05-03-2009 18:20 gmt revision:0 [head]

http://www.mattryall.net/blog/2008/11/wiki-visualisations-with-javascript -- way cool!!

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ref: bookmark-2006.07 tags: BMI BCI EEG bibliography Stephan Scott date: 09-07-2008 19:54 gmt revision:2 [1] [0] [head]



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ref: bookmark-0 tags: monte_carlo MCMC particle_filter probability bayes filtering biblography date: 0-0-2007 0:0 revision:0 [head]

http://www-sigproc.eng.cam.ac.uk/smc/papers.html -- sequential monte carlo methods. (bibliography)

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ref: bookmark-0 tags: graffiti art urban photography date: 0-0-2006 0:0 revision:0 [head]

http://www.beautifulcrime.com/public/exhibitions/ Need flash to view the site.