Monolithically Integrated μLEDs on Silicon Neural Probes for High-Resolution Optogenetic Studies in Behaving Animals

Wu, Stark, Ku, Wise, Buzsáki, Yoon · Neuron · 2015 · neuroscience · 10.1016/j.neuron.2015.10.032 · record Wu2015-monolithically-integrated-leds-on-silicon-ne
tag layer · index · concepts · authors · עברית
Where this record's text came from. faceted 2026-08 by reading the locally held text (xml); every evidence string verified as an exact substring of that text before merging. Claim type is 'method' because the paper's headline contribution is a fabrication approach and device, even though it also reports two substantive neurophysiological findings (radiatum illumination drives spiking more efficiently than oriens; induced ripple properties depend on input locus). The device paper contains both a heat-transfer simulation and in vivo recordings; method is coded 'system-or-tool-building' as the dominant activity. 2026-08-13, 2026-08-15 and 2026-08-25 schema-0.3 passes: every quote verified as an exact substring of the staged text and anchored at merge time; concept terms verified present; every edge endpoint an existing node.
3 quotations on this page contain a reference number where the paper printed a superscript. This journal style prints citations as raised numerals — parameters12,13 — and the extraction flattened them into the line, so the sentence reads parameters 12 , 13 . The digits are citation markers and not part of what the author wrote. The quotes keep them for the same reason they keep every other extraction fault: a quote is reproduced exactly or it proves nothing.
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Other fields define these differently the same word, defined another way in another discipline
principal component analysis 5 fields

Tags on this paper

Every tag the record carries, each linking to every other paper in the corpus that carries it. A tag appears here whether or not its words occur in the article — the spans below are only the ones a sentence in this paper licenses. Of the 22 concept tags on this paper, none is grounded in a quoted sentence. All carry the tagger's gloss of what the term means in this paper, which is not something the article can license.
μLED silicon sapphire InGaN etendue plug efficiency internal quantum efficiency total internal reflection ChR2 recording electrodes CA1 pyramidal stratum radiatum stratum oriens spiking gain jitter iHFOs ripple PYR INT micro-drive opsin expression light reaching non-somatic (dendritic) ChR2 recruits the neuron even when the micro-LED is far from its soma, which smooths the gain-versus-distance relation into a graded rather than step-like profile current flow through the micro-LED raises the voltage of the continuous n-GaN cathode layer, which capacitively couples into the recording interconnects running above it and produces the rectified artifact on all channels excitatory drive arriving at stratum radiatum from CA3 recruits a faster and spatially tighter ripple-generating network than drive arriving at stratum oriens from entorhinal cortex/amygdala threshold temperature spiking gain spike phase temporal jitter voltage command input site locus of maximal iHFO power rank correlation rank correlations permutation test Mann-Whitney U test binomial test exact Binomial test partial correlation partial rank correlation principal component analysis Gaussian mixture model significance level system-or-tool-building

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second readingalternativesan independent re-reading of a facet, recorded whether or not it agrees
relation to other workclaim_relationshow this paper stands to another: agrees, contradicts, extends, qualifies
claim typeclaim_typethe shape of the claim: existence, mechanism, method, critique, prediction, null
concept edgeconcept_edgesan asserted relation between two concepts, with the sentence asserting it
content tagcontent_tagsa finding, definition, quantity, statistic or variable named in the paper
contributioncontributionwhat the paper claims to add
controlcontrolsan experiment run to eliminate a rival explanation
limitationlimitationswhat the paper says its evidence cannot support
mechanismmechanismshow the reported effect is said to come about
methodmethodhow the paper produced its evidence
object of studyobject_of_studywhat the paper is about — the thing it investigates
phenomenonphenomenonthe effect or regularity under study
research questionresearch_questionthe question the paper sets itself
sensesensesa distinct use of a term, quoted where the paper fixes it
transfertransfersa method or concept carried in from another field

The paper

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Every tag on this page

alternatives 3 · claim_relations 9 · claim_type 1 · concept_edges 6 · content_tags 66 · contribution 1 · controls 1 · limitations 10 · mechanisms 8 · method 1 · object_of_study 1 · phenomenon 1 · research_question 1 · senses 5 · transfers 5

Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; none of 6 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.

facettagfieldconf.whose words
object_of_studyhow to deliver light at the scale of a single neuron and record from the same place, in a freely moving animal
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object_of_studythe paper's words
research_questionwhether light sources small enough to match a soma can be built onto a silicon recording probe without excessive heating
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research_questionthe paper's words
contributiona probe with twelve neuron-sized LEDs and thirty-two recording sites on one silicon shank array, driving spikes at 60 nW and moving the resolution limit from light delivery onto opsin targeting
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contributionthe paper's words
claim_typemethod
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claim_typethe paper's words
phenomenonoptogenetic light delivery and recording in deep brain structures of freely moving animals
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phenomenonthe paper's words
methodsystem-or-tool-building
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methodthe paper's words
mechanismsmechanisms
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mechanisms[0]the tagger's words
mechanismsmechanisms
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mechanisms[1]the tagger's words
mechanismsmechanisms
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mechanisms[2]the tagger's words
mechanismscoupling an LED into a waveguide is capped by etendue, which is why the light source is put at the site instead of piped to it
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mechanisms[3]1.0the tagger's words
mechanismssilicon is chosen for three separate reasons at once: it can be micromachined into needles, it conducts heat five times better than sapphire, and being opaque it confines emission to one face
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mechanisms[4]1.0the tagger's words
mechanismsheat leaves through the shank toward the proximal end, so the most distal LED is the worst case and is the one modelled
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mechanisms[5]1.0the tagger's words
mechanismsthe graded fall-off of drive with distance implies light is acting on dendrites, not only somata
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mechanisms[6]0.9the tagger's words
mechanismsthe artefact has two physically distinct sources - voltage coupling on the board and capacitive coupling from the continuous n-GaN layer - and each has its own fix
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mechanisms[7]1.0the tagger's words
limitationsDriving the μLEDs induces low-frequency electrical artifacts on the recording channels.
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what this limits: the recorded signal during stimulation: A LIMITATION OF THE CURRENT VERSION OF uLED PROBES IS THE LOW-FREQUENCY ARTIFACTS INDUCED DURING PERIODIC ACTIVATION
limitations[0]the tagger's words
limitationsNon-somatic opsin expression, not the light source, now caps the achievable spatial resolution of spiking control.
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what this limits: the achievable spatial resolution: THE FINAL LIMITATION TO THE CURRENT UTILITY OF THE uLED PROBES RELATES TO THE AVAILABLE OPSIN TECHNOLOGIES
limitations[1]the tagger's words
limitationsThe probe reports spiking only, so it complements rather than replaces intracellular and all-optical methods.
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what this limits: what the probe can report at all: IT ONLY PROVIDES INFORMATION ABOUT SPIKING (AND NOT ABOUT INTRACELLULAR CALCIUM, Vm, OR TRANSMEMBRANE CURRENTS)
limitations[2]the tagger's words
limitationsThe indirect test of heating effects on spike waveforms is weakened by concurrent high-frequency oscillations at high power.
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what this limits: the heating test on spike waveforms: HIGH-POWER ILLUMINATION WAS OCCASIONALLY ACCOMPANIED BY HIGH-FREQUENCY (2 kHz) OSCILLATIONS, LIMITING THE INTERPRETATIONAL POWER OF THESE OBSERVATIONS
limitations[3]the tagger's words
limitationsphoton extraction is poor by construction: 33% internal efficiency, half the light lost into the substrate, most of the rest trapped by total internal reflection
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what this limits: the light budget: APPROXIMATELY 50% OF THE PHOTONS ARE EMITTED TOWARD THE SUBSTRATE AND ARE ABSORBED AT THE GaN/SILICON INTERFACE
limitations[4]1.0the tagger's words
limitationsperiodic driving injects a low-frequency artefact into the recordings, present in opsin-free animals and removed only by offline filtering
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what this limits: the same scope as limitations[0] - the artefact is present in opsin-free animals and removed by filtering, not absent
limitations[5]1.0the tagger's words
limitationsthere is no accepted safe-temperature standard for implanted devices, so the 1 degree threshold used here is the authors' own
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what this limits: every safety claim about the device: AS THERE IS NO ACCEPTED THRESHOLD TEMPERATURE FOR THE SAFE OPERATION OF IMPLANTABLE NEURAL DEVICES, WE LOOSELY DEFINE THE THRESHOLD AS 1 degree - the criterion is the authors' own
limitations[6]1.0the tagger's words
limitationswhether a few milliseconds above 38 degrees harms the adjacent network is stated as unknown
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what this limits: operation above 3.85 V: THE PEAK TEMPERATURE CAN TRANSIENTLY REACH 38 DEGREES C; HOWEVER, WHETHER A FEW MILLISECONDS OF HEATING BEYOND 38 DEGREES C HAS ADVERSE EFFECT ON THE ADJACENT NEURAL NETWORK IS UNKNOWN
limitations[7]1.0the tagger's words
limitationsthe probe reports spiking only, not calcium, membrane potential or currents, and is offered as complementary rather than superior
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what this limits: the same scope as limitations[2] - spiking only, offered as complementary rather than replacement
limitations[8]1.0the tagger's words
limitationsspatial resolution is now limited by where the opsin is expressed rather than by where the light goes
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what this limits: the same scope as limitations[1]: NON-SOMATIC OPSIN EXPRESSION FACILITATED MULTILAYERED CONTROL BUT ALSO REDUCED the achievable resolution
limitations[9]1.0the tagger's words
transfersmonolithic on-silicon LED fabrication technology is carried over into implantable neural probes for systems neuroscience
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transfers[0]the tagger's words
transfersthe Pennes bioheat equation, with a blood-perfusion term, is imported to simulate brain tissue heating around the probe
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transfers[1]the tagger's words
transfersmonolithic integration and lithographic patterning, applied so that light sources and electrodes share one substrate
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transfers[2]1.0the tagger's words
transfersetendue, used as the argument for abandoning waveguide coupling altogether
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transfers[3]1.0the tagger's words
transfersfinite-element bio-heat modelling, used to set an operating envelope before any animal was implanted
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transfers[4]1.0the tagger's words
controlsrecording during μLED voltage bias in saline and in wild-type animals
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eliminates: that the time-locked artifacts in the wide-band traces are neural responses driven by the light, rather than electrical artifacts of the μLED drive itself · outcome: held
controls[0]0.9the tagger's words
sensesspiking gain here = firing rate during light divided by the same neuron's rate without light, so it is a within-neuron ratio and not a comparison across cells
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senses[0]1.0the tagger's words
sensesplug efficiency = optical power out over electrical power in; the paper gives both a measured value (0.87%) and a value derived from the loss chain (1.1%), so the measurement is checkable
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senses[1]1.0the tagger's words
sensesiHFO is used exactly as Stark2014 defined it - an induced high-frequency oscillation - and is treated here as a proxy for somatic drive because population synchrony averages out dendritic effects
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senses[2]1.0the tagger's words
sensesdirect versus indirect activation is a CLASSIFICATION, assigned by a Gaussian mixture model over waveform features, not an observation
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senses[3]1.0the tagger's words
sensesthe safe threshold is a 1 degree rise, defined by these authors for want of a field standard and described by them as loose
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senses[4]1.0the tagger's words
alternativesclaim_type: method
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a second reading reaching the same value. Recorded: method — note: a second reading reaching the same value from a different sentence. Not applied - a person decides.
alternatives.claim_typethe tagger's words
alternativesmethod: monolithic fabrication of InGaN LEDs on silicon, bio-heat modelling, and in vivo recording from CA1 of anaesthetised and freely moving mice with opsin-free controls
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a second reading DIFFERING from the recorded value. Recorded: system-or-tool-building — note: a second reading, verbatim-verified, disagreeing with the value on the record. Not applied - a person decides.
alternatives.methodthe tagger's words
alternativesphenomenon: optogenetic control of spiking at cellular spatial resolution in the intact brain
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a second reading DIFFERING from the recorded value. Recorded: optogenetic light delivery and recording in deep brain structures of freely moving animals — note: a second reading, verbatim-verified, disagreeing with the value on the record. Not applied - a person decides.
alternatives.phenomenonthe tagger's words
claim_relationsbuilds-on → Wu et al., 2013
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claim_relations[0]the tagger's words
claim_relationsextends → Kim et al., 2013; McAlinden et al., 2013
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claim_relations[1]the tagger's words
claim_relationsextends → Stark et al., 2014
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claim_relations[2]the tagger's words
claim_relationsextends → Stark et al. 2014, by inducing high-frequency oscillations with focal rather than fibre illumination
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claim_relations[3]1.0the tagger's words
claim_relationscritiques → fibre-coupled optogenetic probes, whose resolution is set by the bulk of the implanted fibre
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differs in: THE AXIS IS THE PHYSICAL BULK OF THE LIGHT DELIVERY. 'Early work involving in vivo optogenetics relied on manual assembly of commercially available recording components such as metal electrodes or passive high-density probes (STARK ET AL., 2012) with optical fibers, which are bulky and may suffer from misalignment errors. Moreover, the spatial resolution of fiber-based optogenetic devices is limited by the bulk of the [fibre].' Note the citation: this criticises the very device whose own paper names heat, a 60 um recording radius and over-precision as its limits. FOUR DIFFERENT AXES ON ONE INSTRUMENT, THREE OF THEM FROM ITS OWN AUTHORS.
claim_relations[4]1.0the tagger's words
claim_relationscritiques → sapphire-substrate microLED probes, which scatter light and cannot be machined into needles
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differs in: THE AXIS IS THE SUBSTRATE MATERIAL, AND IT COSTS TWICE. 'Quotation withheld.' One material choice degrades the measurement AND the tissue - so the comparison is not between two devices' performance but between what each material permits.
claim_relations[5]1.0the tagger's words
claim_relationscritiques → injectable polymer LED devices, too wide for cellular resolution and hard to mount on a microdrive
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claim_relations[6]1.0the tagger's words
claim_relationsconfirms → activation thresholds reported for manually assembled diode probes
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claim_relations[7]1.0the tagger's words
claim_relationsdistinguishes-from → two-photon holographic and intracellular methods, which cannot reach deep structures in freely moving animals
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differs in: THE AXIS IS WHETHER THE METHOD REACHES A FREELY MOVING ANIMAL. 'Such high spatial resolution control over spiking has been previously possible only by intra-cellular current injection or by two-photon microscopy combined with optogenetics. Intracellular methods are not yet scalable in freely moving animals.' The resolution is granted to the existing methods; what they lack is the preparation - so a claim about what is achievable needs the animal state attached.
claim_relations[8]1.0the tagger's words
concept_edgesμLED —part-of→ silicon
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strength of the relation: 1 · note: monolithic integration is the whole claim: the light source is built on the probe rather than coupled to it Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the uLEDs are fabricated monolithically on silicon; part-of is loose.
also in: μLED · silicon
concept_edges[0]1.0the tagger's words
concept_edgessilicon —contrasted-with→ sapphire
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strength of the relation: 1 · note: CRITERION: three at once - machinable into needles, five times the thermal conductivity, and opaque so emission stays on one face Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span lists limits of a sapphire substrate beside a silicon probe; contrasted-with is loose.
also in: silicon · sapphire
concept_edges[1]1.0the tagger's words
concept_edgesgain —operationalised-as→ spiking
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strength of the relation: 1 · note: direction is measure-to-phenomenon; the ratio is within-neuron, so it cannot be compared across cells of different baseline Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but spiking 'gain' is DEFINED as a ratio of spiking rates; operationalised-as is loose.
also in: gain · spiking
concept_edges[5]1.0the tagger's words
concept_edgesPYR —contrasted-with→ INT
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strength of the relation: 1 · note: CRITERION: PYR are taken as directly driven and INT as circuit-driven, and PYR jitter is lower at every distance
also in: PYR · INT
concept_edges[6]1.0the tagger's words
concept_edgesstratum radiatum —contrasted-with→ stratum oriens
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strength of the relation: 1 · note: illumination below or at the layer drives spiking better than above it, attributed to dendritic geometry or expression bias
concept_edges[8]1.0the tagger's words
concept_edgesChR2 —causes→ spiking
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strength of the relation: 1 · note: shown by absence in wild-type controls under the same illumination
also in: ChR2 · spiking
concept_edges[10]1.0the tagger's words
content_tagsrank correlation
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content_tags.statistics[0]the tagger's words
content_tagspermutation test
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content_tags.statistics[1]the tagger's words
content_tagsMann-Whitney U test
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content_tags.statistics[2]the tagger's words
content_tagsbinomial test
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also in: binomial test
content_tags.statistics[3]the tagger's words
content_tagspartial correlation
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content_tags.statistics[4]the tagger's words
content_tagsprincipal component analysis
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content_tags.statistics[5]the tagger's words
content_tagsGaussian mixture model
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content_tags.statistics[6]the tagger's words
content_tagssignificance level
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content_tags.statistics[7]the tagger's words
content_tagsrank correlation
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content_tags.statistics[8]1.0the tagger's words
content_tagspermutation test
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content_tags.statistics[9]1.0the tagger's words
content_tagsMann-Whitney U test
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content_tags.statistics[10]1.0the tagger's words
content_tagsGaussian Mixture Model
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content_tags.statistics[11]1.0the tagger's words
content_tagsBinomial test
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also in: Binomial test
content_tags.statistics[12]1.0the tagger's words
content_tagsSub-microwatt light (60 nW) from a single integrated micro-LED was enough to drive spiking, and microwatt-range power drove fast population oscillations.
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content_tags.findings[0]the tagger's words
content_tagsThe probe achieved independent optical control of neurons roughly 50 micrometres apart and of separate somatic versus dendritic compartments of single neurons.
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content_tags.findings[1]the tagger's words
content_tagsIlluminating pyramidal cell bodies and apical dendrites in stratum radiatum drove spiking more effectively than illuminating stratum oriens.
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content_tags.findings[2]the tagger's words
content_tagsWhere the light entered the layer changed the induced ripples: infra- and intra-layer illumination produced the fastest and most vertically compact oscillations, while supra-layer illumination produced slower and more widespread ones.
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content_tags.findings[3]the tagger's words
content_tagsSpiking gain of directly driven pyramidal cells increased with light power and decreased with the distance between the micro-LED and the cell soma.
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content_tags.findings[4]the tagger's words
content_tagsDirectly light-driven pyramidal cells spiked with lower temporal jitter (median 29 ms) than indirectly driven interneurons (46 ms), at every distance bin.
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content_tags.findings[5]the tagger's words
content_tagsThermal simulation indicated that every drive condition below 3.4 V is safe even under ten seconds of continuous operation.
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content_tags.findings[6]the tagger's words
content_tags60 to 120 nW of light drove time-locked spiking in neurons next to a single LED
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content_tags.findings[7]1.0the tagger's words
content_tagstwo LEDs 60 microns apart controlled distinct neurons independently in freely moving mice
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content_tags.findings[8]1.0the tagger's words
content_tagsspiking gain rose with light power and fell with LED-to-soma distance for both directly and indirectly driven cells
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content_tags.findings[9]1.0the tagger's words
content_tagsdirectly driven pyramidal cells had lower spike jitter than indirectly driven interneurons at every distance
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content_tags.findings[10]1.0the tagger's words
content_tagsillumination inside or below the layer produced faster and more compact induced ripples than illumination above it
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content_tags.findings[11]1.0the tagger's words
content_tagsthe graded gain-distance profile implies light is recruiting dendritic opsin, not only somatic
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content_tags.findings[12]1.0the tagger's words
content_tagsspiking was sometimes driven more strongly from stratum oriens than by direct somatic illumination
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content_tags.findings[13]1.0the tagger's words
content_tagsthe measured peak plug efficiency was around 0.87%
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content_tags.findings[14]1.0the tagger's words
content_tagsCONTROL NULL: in opsin-free mice the same illumination changed no action potentials, so the effects are not thermal
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content_tags.findings[15]1.0the tagger's words
content_tagsDECLARED INCONCLUSIVE: the waveform-distortion test of heating was confounded by 2 kHz oscillations at high power
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content_tags.findings[16]1.0the tagger's words
content_tagsthe low-frequency artefact appeared in wild-type animals too and was removed offline rather than at source
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content_tags.findings[17]1.0the tagger's words
content_tagsthreshold temperature
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content_tags.definitions[0]the tagger's words
content_tagsspiking gain
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also in: spiking gain
content_tags.definitions[1]the tagger's words
content_tagsspike phase
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also in: spike phase
content_tags.definitions[2]the tagger's words
content_tagstemporal jitter
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content_tags.definitions[3]the tagger's words
content_tagsgain
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also in: gain
content_tags.definitions[4]1.0the tagger's words
content_tagsplug efficiency
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content_tags.definitions[5]1.0the tagger's words
content_tagsetendue
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also in: etendue
content_tags.definitions[6]0.9the tagger's words
content_tagsinternal quantum efficiency
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content_tags.definitions[7]1.0the tagger's words
content_tagsiHFOs
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also in: iHFOs
content_tags.definitions[8]0.9the tagger's words
content_tagsvoltage command
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content_tags.variables[0]the tagger's words
content_tagsinput site
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also in: input site
content_tags.variables[1]the tagger's words
content_tagsspiking gain
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also in: spiking gain
content_tags.variables[2]the tagger's words
content_tagstemporal jitter
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content_tags.variables[3]the tagger's words
content_tagslocus of maximal iHFO power
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content_tags.variables[4]the tagger's words
content_tagsgain
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also in: gain
content_tags.variables[6]1.0the tagger's words
content_tagsjitter
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also in: jitter
content_tags.variables[7]1.0the tagger's words
content_tagsplug efficiency
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.variables[8]1.0the tagger's words
content_tags60 nW — light power sufficient to induce time-locked spiking in nearby neurons
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content_tags.quantities[0]the tagger's words
content_tags150 μm 2 — light-emitting area of a single micro-LED, comparable to a pyramidal soma cross-section
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content_tags.quantities[1]the tagger's words
content_tags12 μLEDs and 32 recording sites — components integrated on each implanted four-shank probe
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content_tags.quantities[2]the tagger's words
content_tags4,096 (2 12 ) — number of distinct on/off combinations of the twelve micro-LEDs that can be programmed at any moment
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content_tags.quantities[3]the tagger's words
content_tags0.87% — measured peak wall-plug (optical out over electrical in) efficiency of a micro-LED
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content_tags.quantities[4]the tagger's words
content_tags3.33% — photon extraction efficiency of the on-silicon micro-LED
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content_tags.quantities[5]the tagger's words
content_tags93 — well-isolated single units recorded from CA1 across six mice
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content_tags.quantities[6]the tagger's words
content_tags53 μW — saturated optical output of a micro-LED at high (~13 mA) injection current
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content_tags.quantities[7]the tagger's words
content_tagsPYR: 29 ms; INT: 46 ms — median spike-timing jitter of directly driven pyramidal cells versus indirectly driven interneurons
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content_tags.quantities[8]the tagger's words
content_tags60 nW — light power sufficient to induce spiking in nearby neurons
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[9]1.0the tagger's words
content_tags150 μm 2 — LED emission area, matched to a pyramidal soma cross-section
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content_tags.quantities[10]1.0the tagger's words
content_tags0.87% against 1.1% — measured plug efficiency against the value derived from the loss chain
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value source note: THE VALUE DRAWS ON THE PAPER BEYOND THIS QUOTE: part of it is printed elsewhere in the paper, not in this quote ('measured peak plug efficiency is around 0.87% ( Figure 3C )…').
content_tags.quantities[11]1.0the tagger's words
content_tags33%, 3.33% — internal quantum efficiency and photon extraction efficiency of the on-silicon LED
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content_tags.quantities[12]1.0the tagger's words
content_tags1 degree — the temperature-rise threshold the authors adopted for want of a field standard
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content_tags.quantities[13]1.0the tagger's words
content_tags2°C–3°C — how much brain temperature moves on its own between rest and activity
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content_tags.quantities[14]1.0the tagger's words
content_tags4,096 — programmable on-off combinations across twelve LEDs
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content_tags.quantities[15]1.0the tagger's words
content_tagsless than 8 μA — current needed to reach the intensity that activates ChR2
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content_tags.quantities[16]1.0the tagger's words
content_tags1 MΩ at 1 kHz — impedance of the integrated recording electrodes
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content_tags.quantities[17]1.0the tagger's words

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