phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | spike sorting for high-density electrode arrays— “Here we describe a system for the spike sorting of high-channel count electrode data, implemented in a suite of freely available software.” | |
| claim-type | method— “Here, we present a set of novel tools to solve this problem, implemented in a suite of practical, user-friendly, open-source software.” | |
| method — evidence | — “We have produced a software suite for spike sorting of data from large, dense electrode arrays.” | |
| object of study — evidence | — “The process of using these waveforms to decipher the firing times of the recorded neurons is known as “spike sorting”” | |
| research question — evidence | — “While the spike sorting problem has attracted considerable theoretical research, our goal was to produce a practical system that can be immediately used by working neurophysiologists. The ability to process large datasets (millions of spikes in hundreds of dimensions) in reasonable human and computer time was deemed essential; error rates… | |
| contribution — evidence | — “However, use of this technology requires the development of techniques for decoding the spike times of the recorded neurons, from the raw data captured from the probes. Here, we present a set of novel tools to solve this problem, implemented in a suite of practical, user-friendly, open-source software. We validate these methods on data from… | |
| transfer | from statistics and machine learning: the EM algorithm for mixtures of Gaussians, modified so that uninformative dimensions are disenfranchised rather than weighted— “To solve this problem, we designed a novel method, the “masked EM algorithm” 30 . This algorithm fits the data as a mixture of Gaussians, but with each feature vector replaced by a virtual ensemble in which features with masks near zero are replaced by a noise distribution (see Methods). Channels with low mask values are thus… | transfers[0] |
| transfer | from image processing: the flood fill, used to grow a spike as a connected component in space and time— “Specifically, spikes are detected as spatiotemporally connected components, in which the filtered signal exceeds a “weak threshold” θ w for every point, and in which at least one point exceeds a “strong threshold”” | transfers[1] |
| transfer | from cluster validation: the Fowlkes-Mallows index, used here to score agreement between two human operators rather than between two clusterings— “We separately assessed consistency on spikes that all operators had identified be in “good” clusters, on spikes that at least one operator had identified to be in a good cluster, and on all remaining spikes. Similarity was assessed with the Fowlkes-Mallows index 31 , which gives a score between 1 for complete agreement, and 0 for complete… | transfers[2] |
| transfer | from connectomics: the precedent that automatic methods in data-intensive science run under human supervision— “A similar situation arises in many fields of data-intensive science: in electron microscopic connectomics, for example, automatic methods can only be used under the supervision of human operators” | transfers[3] |
| mechanism | noise on many uninformative channels swamps signal on few informative channels, so Gaussian-mixture clustering breaks down as dimensionality grows— “The first is the “curse of dimensionality”: in high dimensions, noise measured on the large number of uninformative channels will swamp signals measured on the smaller number of informative channels.” | mechanisms[0] |
| mechanism | probabilistically disenfranchising low-mask channels removes their contribution to cluster assignment and so prevents threshold-crossing artefacts from generating spurious clusters— “Channels with low mask values are thus “disenfranchised”, and do not contribute to cluster assignment; the probabilistic nature of this disenfranchisement means false clusters are not created when amplitudes cross an arbitrary threshold.” | mechanisms[1] |
| mechanism | requiring a strong-threshold crossing inside each weak-threshold connected component discards isolated noise islands while merging weakly connected regions of one spike— “The dual-threshold approach avoids spurious detection of small noise events, since isolated islands in which only the weak threshold is exceeded are not retained.” | mechanisms[2] |
| mechanism | cost scales with unmasked channels per spike rather than total channels, which is why the method stays tractable as arrays grow— “The computational complexity of this algorithm is better than that of the traditional EM algorithm, scaling with the mean number of unmasked channels per spike (which does not increase for larger arrays), rather than the total number of channels.” | mechanisms[3] |
| mechanism | overlapping spikes are separated not by their features, which are nearly identical, but by which channels they appear on - the mask vector— “Second, a “mask vector” is computed from the peak spike amplitude on each detected channel, rescaled and clipped so channels outside the connected component have mask 0, and channels with amplitude above θ s have mask 1. The mask vector allows temporally overlapping spikes to be clustered as separate cells.” | mechanisms[4] |
| mechanism | the curse of dimensionality: on a large array the noise on uninformative channels outweighs the signal on the few informative ones— “The first is the “curse of dimensionality”: in high dimensions, noise measured on the large number of uninformative channels will swamp signals measured on the smaller number of informative channels.” | mechanisms[5] |
| mechanism | masked EM disenfranchises low-mask channels probabilistically, so no false cluster is created when an amplitude happens to cross a threshold— “To solve this problem, we designed a novel method, the “masked EM algorithm” 30 . This algorithm fits the data as a mixture of Gaussians, but with each feature vector replaced by a virtual ensemble in which features with masks near zero are replaced by a noise distribution (see Methods). Channels with low mask values are thus… | mechanisms[6] |
| mechanism | two thresholds rather than one: the weak one prevents a spike being split by noise, the strong one prevents noise being kept as a spike— “The dual-threshold approach avoids spurious detection of small noise events, since isolated islands in which only the weak threshold is exceeded are not retained. Conversely, spikes will not be erroneously split due to noise, as areas joined by weak… | mechanisms[7] |
| mechanism | the human cost of curation is quadratic in clusters unless the software orders the candidate merges, which makes it linear | mechanisms[8] |
| mechanism | complexity scales with unmasked channels per spike, a quantity that does not grow as arrays get bigger | mechanisms[9] |
| builds-on | KlustaKwik, first version (tetrode-oriented hard EM mixture-of-Gaussians program released in 2000) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[0] |
| builds-on | Klusters manual spike-sorting environment (ref. 13) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[1] |
| builds-on | Best Ellipsoid Error Rate (BEER) measure (ref. 8) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[2] |
| extends | semi-automatic tetrode spike sorting, which reached 5% error against intracellular ground truth Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[3] |
| contradicts | the assumption that tetrode sorting methods carry over to large arrays Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[4] |
| critiques | the practice of deciding by eye which units are well isolated Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[5] |
| distinguishes-from | template-matching sorters validated on in vitro retinal arrays Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[6] |
| critiques | the existing literature of proposed sorting methods, none of which was adopted Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[7] |
| contradicts | the strategy of adding time as a clustering feature to track drift Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[8] |
| sense | ground truth here = SIMULATED - a known cell's waveforms added into another recording - not intracellular recording of the same neuron; the word is used for both in this literature Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[0] |
| sense | well-isolated single unit = a cluster an operator accepts; the paper shows this judgement is not shared between operators, so the term does not denote a fixed object Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[1] |
| sense | manual curation = correcting the automatic clustering, not selecting data; it is a required step of the measurement, not a post-hoc filter Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[2] |
| sense | mask vector = which channels a spike appeared on, rescaled to [0,1]; distinct from the feature vector, which is the PCA summary of its shape Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[3] |
| sense | theoretical optimum = the Best Ellipsoid Error Rate, a quadratic decision boundary fitted to ground truth and cross-validated - a benchmark, not a bound on any possible algorithm Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[4] |
| control | every added spike displaced by a RANDOM SUB-SAMPLE OFFSET via cubic spline interpolation before being written into the simulated data — held — rules out the test being passable without sub-sample alignment - spikes added on the sampling grid would let a sorter that ignores sub-sample timing score as well as one that does not, so the benchmark would not test the thing it claims to Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[0] |
| differs in | the practice of deciding by eye which units are well isolated — THE AXIS IS WHO OR WHAT DECIDES ISOLATION QUALITY. 'experienced operators tended to make similar judgements during the manual curation process, but their judgements of which units were well-isolated were subjective ... we therefore recommend that these [quantitative criteria] be used, rather than human judgements.' Note the shape: agreement between operators is granted and is not treated as evidence of correctness - concordance and validity are separated explicitly. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[5] |
| differs in | template-matching sorters validated on in vitro retinal arrays — THE AXIS IS THE NOISE LEVEL OF THE DATA THE METHOD WAS VALIDATED ON. 'TEMPLATE-MATCHING ALGORITHMS HAVE SOLVED THIS PROBLEM IN THE CASE OF IN VITRO RETINAL ARRAY DATA, BUT THESE DATA ARE MUCH LESS NOISY THAN IN VIVO BRAIN RECORDINGS.' The method is granted its success and the success is bounded by the preparation it was demonstrated on - so 'solved' is true of one regime and unproven in the other, and a citation carries only the word. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[6] |
| note | RETRACTED (DIRECTION REVERSED) · manual curation —part-of→ spike sorting — direction is member-to-container: curation is the fourth step of the sorting process, not an optional extra Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[0] |
| retracted | RETRACTED (DIRECTION REVERSED) · manual curation —part-of→ spike sorting — DIRECTION REVERSED. The edge says spike sorting is part of manual curation. The paper says the opposite: '…extraction, (2) cluster analysis, and (3) MANUAL CURATION…' Manual curation is a step OF spike sorting. Found while looking for a span naming both endpoints - the search for grounding surfaced a direction error. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[0] |
| note | masked EM algorithm —contrasted-with→ classical EM algorithm — the same data: masked near the BEER optimum, classical above 50% error Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[1] |
| note | EVIDENCE CORRECTED (RE-GROUNDED) · well-isolated —contrasted-with→ multiunit activity — the boundary the operator study found to be operator-dependent Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[5] |
| retracted | EVIDENCE CORRECTED (RE-GROUNDED) · well-isolated —contrasted-with→ multiunit activity — RE-GROUNDED. The old span was about operator consistency. This sentence names both as the two outcomes of one decision - the operator '…WELL-ISOLATED neuron, OR rejects it as MULTIUNIT ACTIVITY…' - so the contrast is a forced choice rather than an observed difference. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[5] |
| audit | bursting —is-a→ nonstationarity — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the span models bursting as a source of waveform variability; is-a 'nonstationarity' is loose. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[7] |
| weight | bursting —is-a→ nonstationarity — 0.9 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[7] |
| note | silicon probes —contrasted-with→ tetrode — CRITERION, stated: overlapping spikes are extremely common on the dense probe and not on the tetrode Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[10] |
| note | manual curation —part-of→ spike sorting — REPLACES another row of this record, which ran the other way. The convention is from=part, to=whole - 'vertex --part-of--> network'. NO separate quote for the relation: the span's composition cue is 'involves', which is not in CONTAINER_FIRST, and its only other attestation in the corpus (Pickering2008) is fenced. One available occurrence does not earn a cue, so the clause-level check is forgone rather than the rule bent. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[13] |
| audit | mask vector —distinct-from→ feature vector — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span compares the feature vectors and mask vectors of two example spikes; distinct-from is loose. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[14] |
| note | mask vector —distinct-from→ feature vector — RE-GROUNDS another row of this record: the old span named ONE endpoint. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[14] |
| outcome (stated by the tagger, no quotation) | control — held | controls[0] |
| for which use | limitation — the practical claim of usability at scale, not the accuracy results: IT CAN TAKE HOURS OR EVEN DAYS TO COMPLETE ON A STANDARD SINGLE-CORE MACHINE Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[0] |
| for which use | limitation — every spike count and every unit derived from dense-array data: IT CANNOT RESOLVE SPIKES THAT OVERLAP IN BOTH SPACE AND TIME - those spikes are absent from the output Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[1] |
| for which use | limitation — any claim that a set of well-isolated single units is operator-independent: THEIR JUDGEMENTS OF WHICH UNITS WERE WELL-ISOLATED WERE SUBJECTIVE Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[2] |
| for which use | limitation — the same scope as limitations[1] - spatiotemporally overlapping spikes are unresolved Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[3] |
| for which use | limitation — the accuracy figures only, which are measured against this truth set: WE CREATED A SIMULATED GROUND TRUTH DATASET ... SINCE THE EXTRACELLULAR MEDIUM IS A LINEAR CONDUCTOR - the validation assumes linearity Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[4] |
| for which use | limitation — the generalisation of those accuracy figures to real bursting cells: THE INTERSPIKE INTERVALS TYPICAL OF BURSTING NEURONS WERE NOT SIMULATED Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[5] |
| for which use | limitation — the reproducibility of the unit yield between labs: THE JUDGEMENT OF WHETHER A CLUSTER SHOULD BE CONSIDERED A WELL-ISOLATED SINGLE UNIT was not consistent across operators Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[6] |
| for which use | limitation — any expectation that manual curation can be removed: WAVEFORMS ARE NOT CONSTANT, BUT CHANGE ACCORDING TO FIRING - the errors forcing manual correction resist modelling Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[7] |
| for which use | limitation — the same scope as limitations[0] - runtime, not accuracy Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[8] |
| for which use | limitation — the prospect of solving the overlap problem by template matching: SUCH METHODS ARE NOT AT PRESENT WIDELY APPLIED TO IN VIVO RECORDINGS Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[9] |
| replication | untested | |
| limitation | Clustering can still take hours or days on large datasets with a single-core machine. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[0] |
| limitation | Spikes that overlap in both space and time cannot be resolved by the detection algorithm. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[1] |
| limitation | Operators' judgements of which clusters count as well-isolated units are subjective, so the pipeline still depends on a non-reproducible human step. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[2] |
| limitation | spikes that overlap in both space and time cannot be resolved at all Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[3] |
| limitation | ground truth is simulated, and rests on the assumption that the extracellular medium is a linear conductor so waveforms can simply be added Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[4] |
| limitation | the bursting interspike intervals that make real spike trains hard were deliberately not simulated Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[5] |
| limitation | which clusters count as well-isolated single units is not reproducible between operators Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[6] |
| limitation | the waveform changes that force manual correction have resisted mathematical modelling Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[7] |
| limitation | runtime can reach hours or days on a single core Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[8] |
| limitation | template matching, which would solve the overlap problem, is blocked less by the algorithm than by what it would do to the curation step Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[9] |
finding · quantity · variable · definition · key-term — grounded in the full text| finding | Detection is close to optimal with a strong threshold of 4 SD, a weak threshold of 2 SD and a power weight of 2. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[0] |
| finding | The masked EM clustering algorithm reaches roughly 5% false positive and false discovery rates, close to the theoretical optimum. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[1] |
| finding | The classical EM algorithm failed on high-count probe data with error rates above 50%, whereas the masked EM algorithm matched the BEER-estimated optimum. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[2] |
| finding | Human operators agreed with each other about which clusters to merge but disagreed about which clusters count as well-isolated, so quantitative isolation metrics should replace that judgement. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[3] |
| finding | Spacing recording sites further apart than 40 μm substantially degrades sorting performance in rat cortex. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[4] |
| finding | The two sides of a staggered shank act as largely independent probes, so the gain from two-sided shanks is more recorded units rather than better isolation of any one unit. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[5] |
| finding | Adding time as an extra clustering feature to track amplitude drift made clustering worse rather than better. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[6] |
| finding | Manual curation time grows linearly with cluster count at roughly one minute per cluster and is independent of probe size. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[7] |
| finding | the masked EM algorithm is statistically indistinguishable from the theoretical optimum, while the classical EM is far from it Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[8] |
| finding | false positive and false discovery rates are both about 5% Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[9] |
| finding | experienced operators agree on merges, but disagree on which clusters count as well isolated Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[10] |
| finding | the authors therefore recommend quantitative isolation metrics in place of the human judgement Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[11] |
| finding | adding time as a clustering feature to track drift made performance worse, against expectation Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[12] |
| finding | performance in rat cortex falls substantially once site spacing exceeds the 40um same-side spacing of the test probes Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[13] |
| finding | the two sides of a staggered shank work independently: the gain is more units, not better isolation Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[14] |
| finding | detection parameters optimal in cortex were also optimal in CA1 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[15] |
| finding | the classical EM failure is not a parameter choice - rerunning across penalty values could not fix it Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[16] |
| quantity | 5% — error rate the whole pipeline achieves on validation data across species and brain regions Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[0] |
| quantity | 95% — proportion of ground-truth (hybrid) spikes correctly detected at the chosen parameters, with 0.5-sample timing jitter Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[1] |
| quantity | p = 0.8 — t-test comparing masked EM total error to theoretical optimum (no difference), versus p = 0.005 for masked vs classical EM Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[2] |
| quantity | p=0.75 — two-sample t-test showing a cell that stopped firing halfway through the recording did not change total sorting error Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[3] |
| quantity | below 80% — average correct spike-detection rate once alternating recording sites were removed (site thinning) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[4] |
| quantity | over 320 scientists in 50 neurophysiology labs — size of the user base whose feedback shaped the software Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[5] |
| quantity | over 10,000% — speed increase of the reimplemented KlustaKwik clustering program Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[6] |
| quantity | 5% — false positive and false discovery rate of the masked EM algorithm on hybrid data Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[7] |
| quantity | over 50% — error rate of the classical EM algorithm on the same data Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[8] |
| quantity | 4 SD and 2 SD — optimal strong and weak detection thresholds, with power weight 2 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[9] |
| quantity | 95% — spikes correctly detected at those settings, with 0.5 samples of timing jitter Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[10] |
| quantity | below 80% — correct detection after site thinning - the cost of halving electrode density Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[11] |
| quantity | 40 — micron same-side site spacing beyond which performance in rat cortex falls off Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[12] |
| quantity | about 1 minute per cluster — operator time for curation, linear in cluster count and independent of probe size Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[13] |
| quantity | 8 — human operators tested, 5 experienced and 3 novices Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[14] |
| quantity | 6 of 10 — hybrid cells detectable on only one side of a staggered probe Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[15] |
| quantity | over 320 scientists in 50 neurophysiology labs — the user base whose feedback shaped the software Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[16] |
| quantity | 10-20 — simultaneously recorded cells a tetrode can reveal, against one or two for a sharp electrode Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[17] |
| variable | fraction of hybrid spikes detected (dependent) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[1] |
| variable | spike timing jitter (dependent) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[2] |
| variable | mask accuracy (dependent) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[3] |
| variable | site thinning (independent) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[4] |
| variable | weak threshold Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[6] |
| variable | strong threshold Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[7] |
| variable | site spacing Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[8] |
| variable | penalty parameter Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[10] |
| definition | spike sorting Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[0] |
| definition | hybrid spikes Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[1] |
| definition | masked EM algorithm Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[2] |
| definition | mask vector Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[3] |
| definition | Wizard Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[4] |
| definition | spike sorting Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[5] |
| definition | masked EM algorithm Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[6] |
| definition | mask vector Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[7] |
| definition | Best Ellipsoid Error Rate Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[8] |
| definition | hybrid datasets Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[9] |
| definition | Fowlkes-Mallows index Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[10] |
| definition | curse of dimensionality Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[11] |
| key-terms | spike sorting, manual curation, masked EM algorithm, mask vector, ground truth, hybrid datasets, curse of dimensionality, electrode drift, silicon probes, tetrode, well-isolated, multiunit activity |
| concept | hybrid datasets — not defined in this paper's own words; the simulated-ground-truth construction Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[8] |
| t-test p | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[0] |
| two-sample t-test p | as written: two-sample t-test on total errors Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[1] |
| principal component analysis | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[2] |
| cross-validation | as written: evaluates its performance with cross-validation Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[3] |
| standard deviation SD | as written: multiples of the standard deviation of the filtered signal Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[4] |
| robust estimator (median absolute deviation) | as written: a robust estimator, median(| V |)/.6745 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[5] |
| Bayesian Information Criterion BIC | as written: a modification of the Bayesian Information Criterion Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[6] |
| maximum likelihood estimation (mixture of Gaussians) | as written: a hard EM algorithm for maximum-likelihood fitting of a mixture of arbitrary-covariance Gaussians Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[7] |
| false discovery rate / true positive rate | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[8] |
| Fowlkes-Mallows index (clustering agreement) | as written: Fowlkes-Mallows index 31 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[9] |
| t-test | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[10] |
| principal component analysis | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[11] |
| mixture of Gaussians | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[12] |
| cross-validation | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[13] |
| ROC curve | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[14] |
| Bayesian Information Criterion | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[15] |
| Fowlkes-Mallows index | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[16] |
| Kullback-Leibler divergence | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[17] |
| false discovery rate | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[18] |
| geometric random walk | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[19] |
| claim type | method — a second reading reaching the same value; recorded: method Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | alternatives.claim_type |
| method | algorithm design validated on simulated ground truth built by adding a donor cell's waveforms into a second recording, plus a study of 8 human operators curating the same dataset — a second reading DIFFERING from the recorded value; recorded: system-or-tool-building Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | alternatives.method |
| phenomenon | spike sorting: the inference from extracellular waveforms to the identity of the neuron that produced them — a second reading DIFFERING from the recorded value; recorded: spike sorting for high-density electrode arrays Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | alternatives.phenomenon |
When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.
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