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[0] Schmidt EM, McIntosh JS, Durelli L, Bak MJ, Fine control of operantly conditioned firing patterns of cortical neurons.Exp Neurol 61:2, 349-69 (1978 Sep 1)[1] Serruya MD, Hatsopoulos NG, Paninski L, Fellows MR, Donoghue JP, Instant neural control of a movement signal.Nature 416:6877, 141-2 (2002 Mar 14)[2] Fetz EE, Operant conditioning of cortical unit activity.Science 163:870, 955-8 (1969 Feb 28)[3] Fetz EE, Finocchio DV, Operant conditioning of specific patterns of neural and muscular activity.Science 174:7, 431-5 (1971 Oct 22)[4] Fetz EE, Finocchio DV, Operant conditioning of isolated activity in specific muscles and precentral cells.Brain Res 40:1, 19-23 (1972 May 12)[5] Fetz EE, Baker MA, Operantly conditioned patterns on precentral unit activity and correlated responses in adjacent cells and contralateral muscles.J Neurophysiol 36:2, 179-204 (1973 Mar)

[0] Fetz EE, Volitional control of neural activity: implications for brain-computer interfaces.J Physiol 579:Pt 3, 571-9 (2007 Mar 15)

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ref: -0 tags: tennenbaum compositional learning character recognition one-shot learning date: 02-23-2021 18:56 gmt revision:2 [1] [0] [head]

One-shot learning by inverting a compositional causal process

  • Brenden Lake, Russ Salakhutdinov, Josh Tennenbaum
  • This is the paper that preceded the 2015 Science publication "Human level concept learning through probabalistic program induction"
  • Because it's a NIPS paper, and not a science paper, this one is a bit more accessible: the logic to the details and developments is apparent.
  • General idea: build up a fully probabilistic model of multi-language (omniglot corpus) characters / tokens. This model includes things like character type / alphabet, number of strokes, curvature of strokes (parameterized via bezier splines), where strokes attach to others (spatial relations), stroke scale, and character scale. The model (won't repeat the formal definition) is factorized to be both compositional and causal, though all the details of the conditional probs are left to the supplemental material.
  • They fit the complete model to the Omniglot data using gradient descent + image-space noising, e.g tweak the free parameters of the model to generate images that look like the human created characters. (This too is in the supplement).
  • Because the model is high-dimensional and hard to invert, they generate a perceptual model by winnowing down the image into a skeleton, then breaking this into a variable number of strokes.
    • The probabilistic model then assigns a log-likelihood to each of the parses.
    • They then use the model with Metropolis-Hastings MCMC to sample a region in parameter space around each parse -- and they extra sample ψ\psi (the character type) to get a greater weighted diversity of types.
      • Surprisingly, they don't estimate the image likelihood - which is expensive - they here just re-do the parsing based on aggregate info embedded in the statistical model. Clever.
  • ψ\psi is the character type (a, b, c..), ψ=κ,S,R\psi = { \kappa, S, R } where kappa are the number of strokes, S is a set of parameterized strokes, R are the relations between strokes.
  • θ\theta are the per-token stroke parameters.
  • II is the image, obvi.
  • Classification task: one image of a new character (c) vs 20 characters new characters from the same alphabet (test, (t)). In the 20 there is one character of the same type -- task is to find it.
  • With 'hierarchical bayesian program learning', they not only anneal the type to the parameters (with MCMC, above) for the test image, but they also fit the parameters using gradient descent to the image.
    • Subsequently parses the test image onto the class image (c)
    • Hence the best classification is the one where both are in the best agreement: argmaxcP(c|t)P(c)P(t|c)\underset{c}{argmax} \frac{P(c|t)}{P(c)} P(t|c) where P(c)P(c) is approximated as the parse weights.
      • Again, this is clever as it allows significant information leakage between (c) and (t) ...
      • The other models (Affine, Deep Boltzman Machines, Hierarchical Deep Model) have nothing like this -- they are feed-forward.
  • No wonder HBPL performs better. It's a better model of the data, that has a bidirectional fitting routine.

  • As i read the paper, had a few vague 'hedons':
    • Model building is essential. But unidirectional models are insufficient; if the models include the mechanism for their own inversion many fitting and inference problems are solved. (Such is my intuition)
      • As a corrolary of this, having both forward and backward tags (links) can be used to neatly solve the binding problem. This should be easy in a computer w/ pointers, though in the brain I'm not sure how it might work (?!) without some sort of combinatorial explosion?
    • The fitting process has to be multi-pass or at least re-entrant. Both this paper and the Vicarious CAPTCHA paper feature statistical message passing to infer or estimate hidden explanatory variables. Seems correct.
    • The model here includes relations that are conditional on stroke parameters that occurred / were parsed beforehand; this is very appealing in that the model/generator/AI needs to be flexibly re-entrant to support hierarchical planning ...

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ref: -2011 tags: two photon cross section fluorescent protein photobleaching Drobizhev gcamp date: 11-04-2020 18:07 gmt revision:9 [8] [7] [6] [5] [4] [3] [head]

PMID-21527931 Two-photon absorption properties of fluorescent proteins

  • Significant 2-photon cross section of red fluorescent proteins (same chromophore as DsRed) in the 700 - 770nm range, accessible to Ti:sapphire lasers ...
    • This corresponds to a S 0S nS_0 \rightarrow S_n transition
    • But but, photobleaching is an order of magnitude slower when excited by the direct S 0S 1S_0 \rightarrow S_1 transition (but the fluorophores can be significantly less bright in this regime).
      • Quote: the photobleaching of DsRed slows down by an order of magnitude when the excitation wavelength is shifted to the red, from 750 to 950 nm (32).
    • See also PMID-18027924
  • Further work by same authors: Absolute Two-Photon Absorption Spectra and Two-Photon Brightness of Orange and Red Fluorescent Proteins
    • " TagRFP possesses the highest two-photon cross section, σ2 = 315 GM, and brightness, σ2φ = 130 GM, where φ is the fluorescence quantum yield. At longer wavelengths, 1000–1100 nm, tdTomato has the largest values, σ2 = 216 GM and σ2φ = 120 GM, per protein chain. Compared to the benchmark EGFP, these proteins present 3–4 times improvement in two-photon brightness."
    • "Single-photon properties of the FPs are poor predictors of which fluorescent proteins will be optimal in two-photon applications. It follows that additional mutagenesis efforts to improve two-photon cross section will benefit the field."
  • 2P cross-section in both the 700-800nm and 1000-1100 nm range corresponds to the chromophore polarizability, and is not related to 1p cross section.
  • This can be useflu for multicolor imaging: excitation of the higher S0 → Sn transition of TagRFP simultaneously with the first, S0 → S1, transition of mKalama1 makes dual-color two-photon imaging possible with a single excitation laser wavelength (13)
  • Why are red GECIs based on mApple (rGECO1) or mRuby (RCaMP)? dsRed2 or TagRFP are much better .. but maybe they don't have CP variants.
  • from https://elifesciences.org/articles/12727

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ref: -0 tags: synaptic plasticity 2-photon imaging inhibition excitation spines dendrites synapses 2p date: 08-14-2020 01:35 gmt revision:3 [2] [1] [0] [head]

PMID-22542188 Clustered dynamics of inhibitory synapses and dendritic spines in the adult neocortex.

  • Cre-recombinase-dependent labeling of postsynapitc scaffolding via Gephryn-Teal fluorophore fusion.
  • Also added Cre-eYFP to label the neurons
  • Electroporated in utero e16 mice.
    • Low concentration of Cre, high concentrations of Gephryn-Teal and Cre-eYFP constructs to attain sparse labeling.
  • Located the same dendrite imaged in-vivo in fixed tissue - !! - using serial-section electron microscopy.
  • 2230 dendritic spines and 1211 inhibitory synapses from 83 dendritic segments in 14 cells of 6 animals.
  • Some spines had inhibitory synapses on them -- 0.7 / 10um, vs 4.4 / 10um dendrite for excitatory spines. ~ 1.7 inhibitory
  • Suggest that the data support the idea that inhibitory inputs maybe gating excitation.
  • Furthermore, co-inervated spines are stable, both during mormal experience and during monocular deprivation.
  • Monocular deprivation induces a pronounced loss of inhibitory synapses in binocular cortex.

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ref: -2013 tags: 2p two photon STED super resolution microscope synapse synaptic plasticity date: 08-14-2020 01:34 gmt revision:3 [2] [1] [0] [head]

PMID-23442956 Two-Photon Excitation STED Microscopy in Two Colors in Acute Brain Slices

  • Plenty of details on how they set up the microscope.
  • Mice: Thy1-eYFP (some excitatory cells in the hippocampus and cortex) and CX3CR1-eGFP (GFP in microglia). Crossbred the two strains for two-color imaging.
  • Animals were 21-40 days old at slicing.

PMID-29932052 Chronic 2P-STED imaging reveals high turnover of spines in the hippocampus in vivo

  • As above, Thy1-GFP / Thy1-YFP labeling; hence this was a structural study (for which the high resolution of STED was necessary).
  • Might just as well gone with synaptic labels, e.g. tdTomato-Synapsin.

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ref: -2019 tags: Vale photostability bioarxiv DNA oragami photobleaching date: 03-10-2020 21:59 gmt revision:5 [4] [3] [2] [1] [0] [head]

A 6-nm ultra-photostable DNA Fluorocube for fluorescence imaging

  • Cy3n = sulfonated version of Cy3.
  • JF549 = azetidine modified version of tetramethyl rhodamine.

Also including some correspondence with the authors:

Me

Nice work and nice paper, thanks for sharing .. and not at all what I had expected from Ron's comments! Below are some comments ... would love your opinion.

I'd expect that the molar absorption coefficients for the fluorocubes should be ~6x larger than for the free dyes and the single dye cubes (measured?), yet the photon yields for all except Cy3N maybe are around the yield for one dye molecule. So the quantum yield must be decreased by ~6x?

This in turn might be from a middling FRET which reduces lifetime, thereby the probability of ISC, photoelectron transfer, and hence photobleaching.

I wonder if in the case of ATTO 647N Cy5 and Cy3, the DNA is partly shielding the fluorphores from solvent (ala ethidium bromide), which also helps with stability, just like in fluorescent proteins. ATTO 647N generates a lot of singlet oxygen, who knows what it's doing to DNA.

Can you do a log-log autocorrelation of the blinking timeseries of the constructs? This may reveal different rate constants controlling dark/light states (though, for 6 coupled objects, might not be interpretable!)

Also, given the effect of DNA shielding, have you compared to free dyes to single-dye cubes other than supp fig 10? The fact that sulfonation made such a huge effect in brightness is suggestive.

Again, these are super interesting & exciting results!

Author

I haven't directly looked at the molar absorption coefficient but judging from the data that I collected for the absorption spectra, there is certainly an increase for the fluorocubes compared to single dyes. I agree that this would be an interesting experiment and I am planning collect data to measure the molar absorption coefficient. I would also expect a ~6 fold increase for the Fluorocubes.

Yes, we suspect homo FRET to help reduce photobleaching. So far we only measured lifetimes in bulk but are planning to obtain lifetime data on the single-molecule level soon.

We also wondered if the DNA is providing some kind of shield for the fluorophores but could not design an experiment to directly test this hypothesis. If you have a suggestion, that would be wonderful.

The log-log autocorrelation of blinking events is indeed difficult to interpret. Already individual intensity traces of fluorocubes are difficult to analyze as many of them get brighter before they bleach. We are also wondering if some fluorocubes are emitting two photons simultaneously. We will hopefully be able to measure this soon.

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ref: -0 tags: Na Ji 2p two photon fluorescent imaging pulse splitting damage bleaching date: 03-10-2020 21:44 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

PMID-18204458 High-speed, low-photodamage nonlinear imaging using passive pulse splitters

  • Core idea: take a single pulse and spread it out to N=2 kN= 2^k pulses using reflections and delay lines.
  • Assume two optical processes, signal SI αS \propto I^{\alpha} and photobleaching/damage DI βD \propto I^{\beta} , β>α>1\beta \gt \alpha \gt 1
  • Then an NN pulse splitter requires N 11/αN^{1-1/\alpha} greater average power but reduces the damage by N 1β/α.N^{1-\beta/\alpha}.
  • At constant signal, the same NN pulse splitter requires N\sqrt{N} more power, consistent with two photon excitation (proportional to the square of the intensity: N pulses of N/N\sqrt{N}/N intensity, 1/N per pulse fluorescence, Σ1\Sigma \rightarrow 1 overall fluorescence.)
  • This allows for shorter dwell times, higher power at the sample, lower damage, slower photobleaching, and better SNR for fluorescently labeled slices.
  • Examine the list of references too, e.g. "Multiphoton multifocal microscopy exploiting a diffractive optical element" (2003)

  • In practice, a pulse picker is useful when power is limited and bleaching is not a problem (as is with GCaMP6x)

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ref: -0 tags: two photon scanning microscope mirror relay date: 01-31-2020 02:46 gmt revision:1 [0] [head]

PMID-24877017 Optimal lens design and use in laser-scanning microscopy

  • Detail careful design of a scanning two-photon microscope, with custom scan lens, tube lens, and standard 25x objective.
  • Near diffraction limited performance for both the scan and tube lenses across a broad excitation range -- 690 to 1400nm.
  • Interestingly, use a parabolic mirror relay to conjugate the two galvos to each other; seems like a good idea, why has this not been done elsewhere?

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ref: -2019 tags: non degenerate two photon excitation fluorophores fluorescence OPO optical parametric oscillator date: 10-31-2019 20:53 gmt revision:0 [head]

Efficient non-degenerate two-photon excitation for fluorescence microscopy

  • Used an OPO + delay line to show that non-degenerate (e.g. photons of two different energies) can induce greater fluorescence, normalized to input energy, than normal same-energy excitation.

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ref: -2015 tags: PaRAC1 photoactivatable Rac1 synapse memory optogenetics 2p imaging mouse motor skill learning date: 10-30-2019 20:35 gmt revision:1 [0] [head]

PMID-26352471 Labelling and optical erasure of synaptic memory traces in the motor cortex

  • Idea: use Rac1, which has been shown to induce spine shrinkage, coupled to a light-activated domain to allow for optogenetic manipulation of active synapses.
  • PaRac1 was coupled to a deletion mutant of PSD95, PSD delta 1.2, which concentrates at the postsynaptic site, but cannot bind to postsynaptic proteins, thus minimizing the undesirable effects of PSD-95 overexpression.
    • PSD-95 is rapidly degraded by proteosomes
    • This gives spatial selectivity.
  • They then exploited the dendritic targeting element (DTE) of Arc mRNA which is selectively targeted and translated in activiated dendritic segments in response to synaptic activation in an an NMDA receptor dependent manner.
    • Thereby giving temporal selectivity.
  • Construct is then PSD-PaRac1-DTE; this was tested on hippocampal slice cultures.
  • Improved sparsity and labelling further by driving it with the Arc promoter.
  • Motor learning is impaired in Arc KO mice; hence inferred that the induction of AS-PaRac1 by the Arc promoter would enhance labeling during learning-induced potentiation.
  • Delivered construct via in-utero electroporation.
  • Observed rotarod-induced learning; the PaRac signal decayed after two days, but the spine volume persisted in spines that showed Arc / DTE hence PA labeled activity.
  • Now, since they had a good label, performed rotarod training followed by (at variable delay) light pulses to activate Rac, thereby suppressing recently-active synapses.
    • Observed both a depression of behavioral performance.
    • Controlled with a second task; could selectively impair performance on one of the tasks based on ordering/timing of light activation.
  • The localized probe also allowed them to image the synapse populations active for each task, which were largely non-overlapping.

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ref: -0 tags: ETPA entangled two photon absorption Goodson date: 09-24-2019 02:25 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

Can we image biological tissue with entangled photons?

How much fluorescence can we expect, based on reasonable concentrations & published ETPA cross sections?

Start with beer's law: A=σLN A = \sigma L N AA = absorbance; LL = sample length, 10 μm, 1e-3 cm; NN = concentration, 10 μmol; σ\sigma = cross-section, for ETPA assume 2.4e18cm 2/molec2.4e-18 cm^2 / molec (this is based on a FMN based fluorophore; actual cross-section may be higher). Including Avogadro's number and 1l=1000cm 31 l = 1000 cm^3 , A=1.45e5A = 1.45e-5

Now, add in quantum efficiency ϕ=0.8\phi = 0.8 (Rhodamine); collection efficiency η=0.2\eta = 0.2 ; and an incoming photon pair flux of I=1e12photons/sec/modeI = 1e12 photons / sec / mode (which roughly about the limit for quantum behavior; n = 0.1 photons / mode; will add this calculation).

F=ϕησLNI=2.3e6photons/secF = \phi \eta \sigma L N I = 2.3e6 photons/sec This is very low, but within practical imaging limits. As a comparison, incoherent 2p imaging creates ~ 100 photons per pulse, of which 10 make it to the detector; for 512 x 512 pixels at 15fps, the dwell time on each pixel is 20 pulses of a 80 MHz Ti:Sapphire laser, or ~ 200 photons.

Note the pair flux is per optical mode; for a typical application, we'll use a Nikon 16x objective with a 600 μm Ø FOV and 0.8 NA. At 800 nm imaging wavelength, the diffraction limit is 0.5 μm. This equates to about 7e57e5 addressable modes in the FOV. Then an illumination of 1e121e12 photons / sec / mode equates to 7e177e17 photons over the whole field; if each photon pair has an energy of 2.75eV,λ=450nm2.75 eV, \lambda = 450 nm , this is equivalent to 300 mW. 100mW is a reasonable limit, hence scale incoming flux to 2.3e172.3e17 pairs /sec.

Hence, the imaging mode is power limited, and not quantum limited (if you could get such a bright entangled source). And right now that's the limit -- for a BBO crystal, circa 1998 experimenters were getting 1e4 photons / sec / mW. So, 2.3e172.3e17 pairs / sec would require 23 GW. Yikes.

More efficient entangled sources have been developed, using periodically-poled potassium titanyl phosphate (PPPTP), which (again assuming linearity) puts the power requirement at 23 MW. This is within the reason of q-switched lasers, but still incredibly inefficient. The down-conversion process is not linear in intensity, which is why Goodson pumps with SHG from a Ti:sapphire to yield ~1e7 photons; but this of induces temporal correlations which increase the frequency of incoherent TPA.

Still, combining PPPTP with a Ti:sapphire laser could result in 1e13 photons / sec, which is sufficient for scanned microscopy. Since the laser is pulsed, it will still be subject to incoherent TPA; but that's OK, the point is to reduce the power going into the animal via larger ETPA cross-section. The answer to above is a tentative yes. Upon the development of brighter entangled sources (e.g. arrays of quantum structures), this can move to fully widefield imaging.

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ref: -0 tags: ETPA entangled two photon absorption Goodson date: 09-19-2019 15:49 gmt revision:13 [12] [11] [10] [9] [8] [7] [head]

Various papers put out by the Goodson group:

And from a separate group at Northwestern:

  • Entangled Photon Resonance Energy Transfer in Arbitrary Media
    • Suggests three orders of magnitude improvement in cross-section relative to incoherent TPA.
    • In SPDC, photon pairs are generated randomly and usually accompanied by undesirable multipair emissions.
      • For solid-state artificial atomic systems with radiative cascades (singled quantum emitters like quantum dots), the quantum efficiency is near unity.
    • Paper is highly mathematical, and deals with resonance energy transfer (which is still interesting)

Regarding high fluence sources, quantum dots / quantum structures seem promising.

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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: -2007 tags: photobleaching GFP date: 09-10-2019 01:42 gmt revision:1 [0] [head]

PMID-17179937 Major signal increase in fluorescence microscopy through dark-state relaxation (2007)

  • 5-25x increase in fluorescence yields.
  • Idea: allow the (dark) triplet states to decay naturally by keeping inter-pulse intervals of illumination greater than 1us.
  • Works for both 1p and 2p.
  • For volume imaging via 2p, I don’t think that 1um decay time is much of an issue; revisit given fluorophores after >1ms!
  • Suggests again that transition from triplet dark state to excited higher state is a prominent or significant cause of photobleaching; also suggests that triple quenching will have limited utility in scanned or pulsed 2p systems (will have more utility in 1p systems, perhaps..)
  • Atto532 dye has low intersystem crossing to the triplet state (1%) [3,5,14] .. humm.
  • 2p total photon emission seems to flatten above 100GW/cm^2 intensity.
  • 2p absorption is easily saturated independent of pulse width: for short pulses, high intensity leads to absorption to T1 state, which has high cross-section to the Tn>1 state; longer pulses give more time for single-photon absorption.
  • τp by m = 200 and hence the pulse energy by 14-fold does not have a considerable effect on G2p. This obviously indicates that the saturation of the S0 → S1 or of the T1 → Tn > 1 excitation eliminates any dependence on pulse peak intensity or energy.

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ref: -2016 tags: fluorescent proteins photobleaching quantum yield piston GFP date: 06-19-2019 14:33 gmt revision:0 [head]

PMID-27240257 Quantitative assessment of fluorescent proteins.

  • Cranfill PJ1,2, Sell BR1, Baird MA1, Allen JR1, Lavagnino Z2,3, de Gruiter HM4, Kremers GJ4, Davidson MW1, Ustione A2,3, Piston DW
  • Model bleaching as log(F)=αlog(P)+clog(F) = -\alpha log(P) + c or k bleach=bI αk_{bleach} = b I^{\alpha} where F is the fluorescence intensity, P is the illumination power, and b and c are constants.
    • Most fluorescent proteins have α\alpha > 1, which means superlinear photobleaching -- more power, bleaches faster.
  • Catalog the degree to which each protein tends to form aggregates by tagging to the ER and measuring ER morphology. Fairly thorough -- 10k cells each FP.

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ref: -2017 tags: neuromorphic optical computing nanophotonics date: 06-17-2019 14:46 gmt revision:5 [4] [3] [2] [1] [0] [head]

Progress in neuromorphic photonics

  • Similar idea as what I had -- use lasers as the optical nonlinearity.
    • They add to this the idea of WDM and 'MRR' (micro-ring resonator) weight bank -- they don't talk about the ability to change the weihts, just specify them with some precision.
  • Definitely makes the case that III-V semiconductor integrated photonic systems have the capability, in MMACs/mm^2/pj, to exceed silicon.

See also :

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ref: -0 tags: nanophotonics interferometry neural network mach zehnder interferometer optics date: 06-13-2019 21:55 gmt revision:3 [2] [1] [0] [head]

Deep Learning with Coherent Nanophotonic Circuits

  • Used a series of Mach-Zehnder interferometers with thermoelectric phase-shift elements to realize the unitary component of individual layer weight-matrix computation.
    • Weight matrix was decomposed via SVD into UV*, which formed the unitary matrix (4x4, Special unitary 4 group, SU(4)), as well as Σ\Sigma diagonal matrix via amplitude modulators. See figure above / original paper.
    • Note that interfereometric matrix multiplication can (theoretically) be zero energy with an optical system (modulo loss).
      • In practice, you need to run the phase-moduator heaters.
  • Nonlinearity was implemented electronically after the photodetector (e.g. they had only one photonic circuit; to get multiple layers, fed activations repeatedly through it. This was a demonstration!)
  • Fed network FFT'd / banded recordings of consonants through the network to get near-simulated vowel recognition.
    • Claim that noise was from imperfect phase setting in the MZI + lower resolution photodiode read-out.
  • They note that the network can more easily (??) be trained via the finite difference algorithm (e.g. test out an incremental change per weight / parameter) since running the network forward is so (relatively) low-energy and fast.
    • Well, that's not totally true -- you need to update multiple weights at once in a large / deep network to descend any high-dimensional valleys.

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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).

  • Pégard 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: Schmidt-1978.09 tags: Schmidt BMI original operant conditioning cortex HOT pyramidal information antidromic date: 03-12-2019 23:35 gmt revision:11 [10] [9] [8] [7] [6] [5] [head]

PMID-101388[0] Fine control of operantly conditioned firing patterns of cortical neurons.

  • Hand-arm area of M1, 11 or 12 chronic recording electrodes, 3 monkeys.
    • But, they only used one unit at a time in the conditioning task.
  • Observed conditioning in 77% of single units and 65% of combined units (multiunits?).
  • Trained to move a handle to a position indicated by 8 annular cursor lights.
    • Cursor was updated at 50hz -- this was just a series of lights! talk about simple feedback...
    • Investigated different smoothing: too fast, FR does not stay in target; too slow, cursor acquires target too slowly.
      • My gamma function is very similar to their lowpass filter used for smoothing the firing rates.
    • 4 or 8 target random tracking task
    • Time-out of 8 seconds
    • Run of 40 trials
      • The conditioning reached a significant level of performance after 2.2 runs of 40 trials (in well-trained monkeys); typically, they did 18 runs/day (720 trials)
  • Recordings:
    • Scalar mapping of unit firing rate to cursor position.
    • Filtered 600-6kHz
    • Each accepted spike triggered a generator that produced a pulse of of constant amplitude and width -> this was fed into a lowpass filter (1.5 to 2.5 & 3.5Hz cutoff), and a gain stage, then a ADC, then (presumably) the PDP.
      • can determine if these units were in the pyramidal tract by measuring antidromic delay.
    • recorded one neuron for 108 days!!
      • Neuronal activity is still being recorded from one monkey 24 months after chronic implantation of the microelectrodes.
    • Average period in which conditioning was attempted was 3.12 days.
  • Successful conditioning was always associated with specific repeatable limb movements
    • "However, what appears to be conditioned in these experiments is a movement, and the neuron under study is correlated with that movement." YES.
    • The monkeys clearly learned to make (increasingly refined) movement to modulate the firing activity of the recorded units.
    • The monkey learned to turn off certain units with specific limb positions; the monkey used exaggerated movements for these purposes.
      • e.g. finger and shoulder movements, isometric contraction in one case.
  • Trained some monkeys or > 15 months; animals got better at the task over time.
  • PDP-12 computer.
  • Information measure: 0 bits for missed targets, 2 for a 4 target task, 3 for 8 target task; information rate = total number of bits / time to acquire targets.
    • 3.85 bits/sec peak with 4 targets, 500ms hold time
    • With this, monkeys were able to exert fine control of firing rate.
    • Damn! compare to Paninski! [1]
  • 4.29 bits/sec when the same task was performed with a manipulandum & wrist movement
  • they were able to condition 77% of individual neurons and 65% of combined units.
  • Implanted a pyramidal tract electrode in one monkey; both cells recorded at that time were pyramidal tract neurons, antidromic latencies of 1.2 - 1.3ms.
    • Failures had no relation to over movements of the monkey.
  • Fetz and Baker [2,3,4,5] found that 65% of precentral neurons could be conditioned for increased or decreased firing rates.
    • and it only took 6.5 minutes, on average, for the units to change firing rates!
  • Summarized in [1].

____References____

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ref: -2019 tags: three photon imaging visual cortex THG chirp NOPA mice GCaMP6 MIT date: 03-01-2019 18:46 gmt revision:2 [1] [0] [head]

PMID-30635577 Functional imaging of visual cortical layers and subplate in awake mice with optimized three photon microscopy

  • Murat Yildirim, Hiroki Sugihara, Peter T.C. So & Mriganka Sur'
  • Used a fs Ti:Saphirre 16W pump into a non-colinear optical parametric amplifier (both from Spectra-Physics) to generate the 1300nm light.
  • Used pulse compensation to get the pulse width at the output of the objective to 40 fS.
    • Three-photon cross section is inverse quadratic in pulse width:
    • NP 3δ(τR) 2(NA 22hcλ) 3 N \sim \frac{P^3 \delta}{(\tau R)^2} (\frac{NA^2}{2hc\lambda})^3
    • P is power, δ\delta is 3p cross-section, τ\tau is pulse width, R repetition rate, NA is the numerical aperture (sixth power of NA!!!), h c and λ\lambda Planks constant, speed of light, and wavelength respectively.
  • Optimized excitation per depth by monitoring damage levels. varied from 0.5nJ to 5 nJ.
  • Imaged up to 1.5mm deep! All the way to the white matter / subplate.
  • Allegedly used a custom scan and tube lens to minimize aberrations in the excitation path (hence improve 3p excitation)
  • Layer 5 neurons are more broadly tuned for orientation than other layers. But the data is not dramatic.
  • Used straightforward metrics for tuning, using a positive and negative bump gaussian fit, then vector averaging to get global orientation selectivity.
  • Interesting that the variance between layers seems higher than between mice.

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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: maleimide azobenzine glutamate photoswitch optogenetics date: 06-16-2014 21:19 gmt revision:0 [head]

PMID-16408092 Allosteric control of an ionotropic glutamate receptor with an optical switch

  • 2006
  • Use an azobenzene (benzine linked by two double-bonded nitrogens) as a photo-switchable allosteric activator that reversibly presents glutamate to an ion channel.
  • PIMD:17521567 Remote control of neuronal activity with a light-gated glutamate receptor.
    • The molecule, in use.
  • Likely the molecule is harder to produce than channelrhodopsin or halorhodopsin, hence less used. Still, it's quite a technology.

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ref: -0 tags: polyimide electrodes ecog japan photosensitive date: 06-28-2013 01:50 gmt revision:0 [head]

PMID-22719725 Photosensitive-polyimide based method for fabricating various neural electrode architectures

  • Yasuhiro X. Kato,1,* Shigeto Furukawa,2 Kazuyuki Samejima,1 Naoyuki Hironaka,2 and Makio Kashino2
  • many typos in this paper (not that I should talk..) Yet still, it's informative.
  • 12um thick photosensitive polyimide + Cr/Au fabrication.
  • Wet etch (photodeveloper).
  • Wet release (ferric chloride) from glass substrate.
  • Soldered a connector to the polyimide w/ stiffener.
  • Note that polyimide tends to shrink (up to 29%) during baking, unlike parylene!
  • Suggest 20-40um diameter neural recording sites; they did not coat.

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ref: -0 tags: optical neural recording photon induced electron transfer date: 01-02-2013 04:25 gmt revision:2 [1] [0] [head]

PMID-22308458 Optically monitoring voltage in neurons by photo-induced electron transfer through molecular wires.

  • Photoinduced electron transfer.
    • About what you would think -- a photon bumps an electron into a higher orbital, and this electron can be donated to another group or drop back down & fluoresce a photon.
  • Good sensitivity: ΔF/F\Delta F/F of 20-27% per 100mV, fast kinetics.
  • Not presently genetically targetable.
  • Makes sense in terms of energy: "A 100-mV depolarization changes the PeT driving force by 0.05 eV (one electron × half of 100-mV potential, or 0.05 V). Because PeT is a thermally controlled process, the value of 0.05 eV is large relative to the value of kT at 300 K (0.026 eV), yielding a large dynamic range between the rates of PeT at resting and depolarized potentials.
  • Why electrochromic dyes have plateaued:
    • "In contrast, electrochromic dyes have smaller delta G values, 0.003 (46) to 0.02 (47) eV, and larger comparison energies. Because the interaction is a photochemically controlled process, the energy of the exciting photon is the comparison energy, which is 1.5–2 eV for dyes in the blue-to-green region of the spectrum. Therefore, PeT and FRET dyes have large changes in energy versus their comparison energy (0.05 eV vs. 0.026 eV), giving high sensitivities; electrochromic dyes have small changes compared with the excitation photon (0.003–0.02 eV vs. 2 eV), producing low voltage sensitivity."

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ref: -0 tags: neural imaging recording shot noise redshirt date: 01-02-2013 02:20 gmt revision:0 [head]

http://www.redshirtimaging.com/redshirt_neuro/neuro_lib_2.htm

  • Shot Noise: The limit of accuracy with which light can be measured is set by the shot noise arising from the statistical nature of photon emission and detection.
    • If an ideal light source emits an average of N photons/ms, the RMS deviation in the number emitted is N\sqrt N .
    • At high intensities this ratio NN\frac{N}{\sqrt N} is large and thus small changes in intensity can be detected. For example, at 10^10 photons/ms a fractional intensity change of 0.1% can be measured with a signal-to-noise ratio of 100.
    • On the other hand, at low intensities this ratio of intensity divided by noise is small and only large signals can be detected. For example, at 10^4 photons/msec the same fractional change of 0.1% can be measured with a signal-to-noise ratio of 1 only after averaging 100 trials.

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ref: Grutzendler-2011.09 tags: two-photon imaging in-vivo neurons recording dendrites spines date: 01-03-2012 01:02 gmt revision:3 [2] [1] [0] [head]

PMID-21880826[0] http://cshprotocols.cshlp.org/content/2011/9/pdb.prot065474.full?rss=1

  • Excellent source of information and references. Go CSH!
  • Possible to image up to 400um deep. PMID-12490949[1]
  • People have used TPLSM imaging for years in mice. PMID-19946265[2]

____References____

[0] Grutzendler J, Yang G, Pan F, Parkhurst CN, Gan WB, Transcranial two-photon imaging of the living mouse brain.Cold Spring Harb Protoc 2011:9, no Pages (2011 Sep 1)
[1] Grutzendler J, Kasthuri N, Gan WB, Long-term dendritic spine stability in the adult cortex.Nature 420:6917, 812-6 (2002 Dec 19-26)
[2] Yang G, Pan F, Gan WB, Stably maintained dendritic spines are associated with lifelong memories.Nature 462:7275, 920-4 (2009 Dec 17)

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ref: work-0 tags: kicadocaml zbuffer comparison picture screenshot date: 03-03-2010 16:38 gmt revision:4 [3] [2] [1] [0] [head]

Simple illustration of Kicadocaml with Z buffering enabled:

and disabled:

I normally use it with Z buffering enabled, but turn it off if, say, I want to clearly see all the track intersections, especially co-linear tracks or zero length tracks. (Probably I should write something to merge and remove these automatically.) Note that in either case, tracks and modules are rendered back-to-front, which effects a Z-sorting of sorts; it is the GPUs Z buffer that is enabled/disabled here.

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ref: -0 tags: kicadocaml screenshot picture date: 03-03-2010 05:53 gmt revision:2 [1] [0] [head]

Aint she pretty?

More shots of the completed board (click for full resolution image):

  • whole thing, all layers.

  • Just the headstage, top and inner layer 2 only

  • Just the headstage, bottom and inner layers 2, 3 and 4.

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ref: picture-0 tags: photo arizona woman desolate fierce determined 1970 NewYorker date: 05-04-2009 20:49 gmt revision:3 [2] [1] [0] [head]

"One shot of [Lee Freidlander's], from 1969, traps an entire landscape of feeling: a boundless American sky, salted with high clouds, plus Freidlander's wife, Maria, with her slightly smiling face - inside the cab of a single truck, layering what we see through the side window with what is reflected in it. I know of long novels that tell you less "

(not the shot above, but just the same - )

some more - http://www.nga.gov.au/SurfaceBeauty/IMAGES/LRG/Fiedlander-1981.954.jpg

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ref: notes-0 tags: wireless nordic headstage bridge neurorecord pictures photo EMG myopen date: 03-12-2009 02:33 gmt revision:4 [3] [2] [1] [0] [head]

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ref: -0 tags: puerto rico rincon photo panorama date: 01-06-2009 23:28 gmt revision:2 [1] [0] [head]

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ref: -0 tags: san_juan puerto rico panorama photo date: 01-06-2009 06:18 gmt revision:4 [3] [2] [1] [0] [head]

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ref: Fetz-2007.03 tags: hot fetz BMI biofeedback operant training learning date: 09-07-2008 18:56 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-17234689[0] Volitional control of neural activity: implications for brain-computer interfaces (part of a symposium)

  • Limits in the degree of accuracy of control in the latter studies can be attributed to several possible factors. Some of these factors, particularly limited practice time, can be addressed with long-term implanted BCIs. YES.
  • Accurate device control under diverse behavioral conditions depends significantly on the degree to which the neural activity can be volitionally modulated. YES again.
  • neurons (50%) in somatosensory (post central) cortex fire prior to volitional movement. interesting.
  • It should also be noted that the monkeys activated some motor cortex cells for operant reward without ever making any observed movements See: Fetz & Finocchio, 1975, PMID-810359.
    • Motor cortex neurons that were reliably associated with EMG activity in particular forelimb muscles could be readily dissociated from EMG when the rewarded pattern involved cell activity and muscle suppression.
    • This may be realated to switching between real and imagined movements.
  • Biofeedback worked well for activating low-threshold motor units in isolation, but not high threshold units; attempts to reverse recruitment order of motor units largely failed to demonstrate violations of the size principle.
  • This (the typical BMI decoding strategy) interposes an intermediate stage that may complicate the relationship between neural activity and the final output control of the device
    • again, in other words: "First, the complex transforms of neural activity to output parameters may complicate the degree to which neural control can be learned."
    • quote: This flexibility of internal representations (e.g. to imagine moving your arm, train the BMI on that, and rapidly directly control the arm rather than gonig through the intermediate/training step) underlies the ability to cognitively incorporate external prosthetic devices in to the body image, and explains the rapid conceptual adaptation to artificial environments, such as virtual reality or video games.
      • There is a high flexibility of input (sensory) and output (motor) for purposes of imagining / simulating movements.
  • adaptive learning algorithms may create a moving target for the robust learning algorithm; does it not make more sense to allow the cortex to work it's magic?
  • Degree of independent control of cells may be inherently contrained by ensemble interactions
    • To the extent that internal representations depend on relationships between the activities of neurons in an ensemble, processing of these representations involves corresponding constraints on the independence of those activities.
  • quote: "These factors suggest that the range and reliability of neural control in BMI might increase significantly when prolonged stable recordings are acheived and the subject can practice under consistent conditions over extended periods of time.
  • Fetz agrees that the limitation is the goddamn technology. need to fix this!
  • there is evidence of favortism in his citations (friends with Miguel??)

humm.. this paper came out a month ago, and despite the fact that he is much older and more experienced than i, we have arrived at the same conclusions by looking at the same set of data/papers. so: that's good, i guess.

____References____

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ref: notes-0 tags: energy carbon CO2 hot water heater. date: 02-25-2008 23:36 gmt revision:2 [1] [0] [head]

How much carbon dioxide (CO2) is released to heat the water for a 5-minute shower?

  1. assumptions
    1. water enters your house at 45F, and you heat it to 100F.
    2. the energy efficiency of your hot water heater is 87%, and we ignore the cost of static thermal losses.
    3. you live in the southeast like me, which is predominantly powered by coal-fired plants. These plants release about 0.8kg/kwh of CO2 ref
    4. transmission of energy from the power plant to your home is 90% efficient
    5. you have a shower head that flows at a rate of 2.2 gallons/minute
  2. result: 2.2gpm -> 138.6 ml/sec -> * 31C temp rise -> 4.2kw -> 0.31kg CO2.
    1. that's about equivalent of driving 4 miles in a 30mpg car. (gasoline CO2 release = 2.4kg/gallon)

  • Interesting analysis. I'm surprised how much CO2 is used by those 5-minutes of delicious, delicious hot shower! --joeyo

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ref: notes-0 tags: two-photon laser imaging fluorescence lifetime imaging FRET GFP RFP date: 01-21-2008 17:23 gmt revision:0 [head]

images/538_1.pdf

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ref: photo-0 tags: picture photo NYC lisa date: 06-03-2007 16:49 gmt revision:0 [head]

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ref: life-0 tags: Japan photos pictures Nathan Misha Kyoto date: 04-21-2007 20:41 gmt revision:1 [0] [head]

Nathan, Misha, and their lives went to Japan for a week to work with the roboticists @ ATR. During the off time, they spent time exploring and photographing Japan. Misha lent me his camera to video record Clementine, and in the process of trying to free up space in the camera's memory, I found these excellent pictures taken by (presumably) Misha. There were other very nice pictures, but they contain Misha, Nathan etc so I excluded them.

the photo below is by far the best.

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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.