Distributed coding of choice, action and engagement across the mouse brain

Steinmetz, Zatka-Haas, Carandini, Harris · Nature · 2019 · neuroscience · 10.1038/s41586-019-1787-x · record Steinmetz2019-distributed-coding-of-choice-action-and-enga
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 existence: the headline contribution is a map of which neurons encoding which variables exist where, not an account of why. The paper also introduces two methodological instruments (reduced-rank kernel regression, combined-conditions choice probability, jPECC), which is captured in claim relations rather than by changing claim_type. Note the small verbatim typo in limitation 2 ("whether visual neurons would be found these “motor” areas") - it is reproduced exactly as printed, not corrected. 2026-08-13 and 2026-08-15 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.
13 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 · engagement 4 fields · logistic regression 3 fields · cross-validation 3 fields · bootstrap 2 fields · generalized linear model 2 fields · and 1 more →

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 18 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.
choice action vision engagement kernel go/nogo passive Miss midbrain forebrain neocortex VISp ZI timing variance contralateral ipsilateral correlate A recurrent loop between forebrain and midbrain choice areas keeps their choice signals simultaneous despite their different encoding schemes Engagement raises subcortical baseline firing toward the threshold at which movements are triggered, so the same stimulus is more likely to release an action Arousal-linked hyperpolarization and reduced spiking in cortex sharpens the signal-to-noise ratio of sensory representations, explaining why engagement suppresses neocortical activity choice-related signal combined-conditions Choice Probability (ccCP) joint Peri-Event Canonical Correlation (jPECC) engagement index Focality index combined-conditions choice probability ‘Action’ kernel ‘Choice’ kernel contrast condition firing rate contralateral visual stimulus contrast pupil area motion energy previous trial reward outcome inter-trial interval ANOVA multi-way ANOVA two-way ANOVA nested ANOVA nested multiple ANOVA test chi-squared test Fisher’s exact test t-test paired t-test Bonferroni correction Bonferroni-corrected alpha value cross-validation held-out data regression reduced rank regression logistic regression generalized linear model GLM with binomial link function bootstrap principal component analysis principal components analysis canonical correlation analysis ROC / Mann-Whitney U statistic area under a receiver operating characteristic (ROC) curve permutation test shuffle test Fisher's exact test cross-validated electrophysiology

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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

The full text is not reproduced here. This article is not cleared for redistribution, so the page carries the tag layer only. Its evidence sentences are withheld; the grounding status remains with each tag, and the article itself is at https://doi.org/10.1038/s41586-019-1787-x. The reading view exists for the papers whose licence permits it.

Every tag on this page

alternatives 3 · claim_relations 7 · claim_type 1 · concept_edges 4 · content_tags 72 · contribution 1 · controls 7 · limitations 10 · mechanisms 8 · method 1 · object_of_study 1 · phenomenon 1 · research_question 1 · senses 19 · transfers 2

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 4 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.

facettagfieldconf.whose words
object_of_studyWHERE the neurons encoding vision, choice, action and behavioral engagement sit - IT IS UNKNOWN HOW THE NEURONS MEDIATING THESE PROCESSES ARE DISTRIBUTED ACROSS BRAIN REGIONS
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object_of_studythe paper's words
research_questionwhich regions carry signals that predict the CHOSEN action rather than merely accompanying movement - NEURONAL SIGNALS THAT CORRELATE WITH ACTION DO NOT NECESSARILY CORRELATE WITH ACTION SELECTION
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research_questionthe paper's words
contributionNEURONS IN NEARLY ALL REGIONS RESPONDED NON-SPECIFICALLY WHEN THE MOUSE INITIATED AN ACTION, BY CONTRAST, NEURONS ENCODING VISUAL STIMULI AND UPCOMING CHOICES OCCUPIED RESTRICTED REGIONS - and CHOICE SIGNALS WERE RARE AND EMERGED WITH INDISTINGUISHABLE TIMING ACROSS REGIONS
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contributionthe paper's words
claim_typeexistence
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claim_typethe paper's words
phenomenonbrain-wide distribution of neural coding for vision, action, choice and task engagement
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phenomenonthe paper's words
methodelectrophysiology
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
methodthe paper's words
mechanismsmechanisms
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[0]the tagger's words
mechanismsmechanisms
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[1]the tagger's words
mechanismsmechanisms
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[2]the tagger's words
mechanismsthe criterion the paper sets itself before measuring anything: TO CARRY SUCH CHOICE-RELATED SIGNALS, A BRAIN REGION MUST CONTAIN NEURONS WHOSE FIRING SELECTIVELY PREDICTS THE CHOSEN ACTION BEFORE THE ACTION OCCURS
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[3]1.0the tagger's words
mechanismsthe design that makes the criterion testable: THE SAME VISUAL STIMULUS COULD THEREFORE LEAD TO EITHER DIRECTION OF TURN, OR TO NO ACTION, ALLOWING US TO DISSOCIATE THE NEURAL CORRELATES OF THE VISUAL STIMULI, OF ACTION INITIATION AND OF ACTION SELECTION
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[4]1.0the tagger's words
mechanismsthe two encodings that differ without differing in time: IN MIDBRAIN NEARLY ALL CHOICE-SELECTIVE NEURONS (53/54, 98%) PREFERRED CONTRALATERAL CHOICES, while forebrain neurons COULD PREFER EITHER CHOICE, giving A DISTINCTIVE 'BILATERAL' ENCODING OF BOTH CHOICES IN THE FOREBRAIN, VERSUS A 'UNILATERAL' ENCODING OF CONTRALATERAL CHOICES IN THE MIDBRAIN
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[5]1.0the tagger's words
mechanismsthe proposed reason engagement helps: ENHANCED ACTIVITY IN SUBCORTICAL AREAS BRINGS ACTIVITY IN THESE REGIONS CLOSER TO THE LEVEL AT WHICH ACTIONS ARE INITIATED, PROVIDING A POTENTIAL MECHANISM FOR INCREASED PROBABILITY OF ACTION IN ENGAGED STATES
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[6]1.0the tagger's words
mechanismsand what the global pre-movement activity cannot be: THESE SIGNALS MAY COMPRISE FORMS OF COROLLARY DISCHARGE, BUT CANNOT REFLECT SENSORY RE-AFFERENCE AS THEY WERE OBSERVED PRIOR TO MOVEMENT ONSET
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mechanisms[7]1.0the tagger's words
limitationsSample sizes were not set by a power analysis.
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
what this limits: every effect size and null in the survey: THE SAMPLE SIZES (n = 10 MICE; n = 39 RECORDING SESSIONS; n = 29,134 NEURONS) WERE NOT DETERMINED WITH A POWER ANALYSIS
limitations[0]the tagger's words
limitationsWhether visual responses in the newly implicated 'motor' choice areas would exist in untrained animals cannot be determined from these data.
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what this limits: the same scope as limitations[7] - whether visual responses in the newly implicated motor choice areas would exist in untrained animals cannot be determined here
limitations[1]the tagger's words
limitationsCircuit mechanisms, omitted regions (cerebellum, brainstem) and generality to other choice tasks all remain for future work.
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what this limits: the mechanistic and anatomical completeness of the survey: FUTURE WORK WILL BE REQUIRED TO DETERMINE THE CIRCUIT MECHANISMS THAT ENFORCE THESE PRINCIPLES
limitations[2]the tagger's words
limitationsThe experimenter was not blinded to the stimulus contrast condition during acquisition or analysis.
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what this limits: the contrast-condition comparisons: THE EXPERIMENTER WAS NOT BLINDED TO CONTRAST CONDITION EITHER DURING DATA ACQUISITION OR DURING ANALYSIS
limitations[3]the tagger's words
limitationsSix of 39 sessions had to be dropped from the choice-probability control analysis for too few usable trials.
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what this limits: the choice-probability control analysis: SIX SESSIONS HAD TO BE EXCLUDED FOR HAVING FEWER THAN 10 TRIALS INCLUDE-ABLE IN THE CP ANALYSIS
limitations[4]the tagger's words
limitationsTHE FRACTION OF CROSS-VALIDATED VARIANCE THE KERNELS EXPLAINED WAS FREQUENTLY SMALL, EVEN FOR NEURONS WHOSE MEAN RATES THEY ACCURATELY PREDICTED (50.2% for one and 13.6% for another)
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what this limits: reading 'this neuron encodes action' as a statement about that neuron's spiking rather than about its trial-averaged rate
limitations[5]1.0the tagger's words
limitationsa quarter of the neurons could not be placed - WE RECORDED FROM 29,134 NEURONS, OF WHICH 22,458 WERE LOCALIZABLE TO ONE OF 42 BRAIN REGIONS
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
what this limits: any per-region count or map: WE RECORDED FROM 29,134 NEURONS ... OF WHICH 22,458 WERE LOCALIZABLE TO ONE OF 42 BRAIN REGIONS
limitations[6]1.0the tagger's words
limitationsthe training may have made the finding - WHETHER VISUAL NEURONS WOULD BE FOUND these ‘motor’ AREAS IN UNTRAINED ANIMALS IS NOT CLEAR FROM THESE DATA
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
what this limits: reading the visual responses in midbrain and striatum as a property of those structures rather than of trained animals
limitations[7]1.0the tagger's words
limitationsthe survey is not the brain - future work must determine HOW THEY EXTEND TO AREAS SUCH AS CEREBELLUM AND BRAINSTEM OMITTED FROM THE CURRENT SURVEY, and THE EXTENT TO WHICH SIMILAR PRINCIPLES GOVERN THE NEURAL CORRELATES OF DIFFERENT CHOICE TASKS
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
what this limits: the brain-wide reading of the survey: future work must determine HOW THEY EXTEND TO AREAS SUCH AS CEREBELLUM AND BRAINSTEM OMITTED FROM THE CURRENT SURVEY
limitations[8]1.0the tagger's words
limitationsthe timing result is a null - WE COULD NOT DISTINGUISH THE TIMING OF CHOICE-RELATED SIGNALS BETWEEN THESE REGIONS, and the recurrent loop is offered as the PARSIMONIOUS explanation of that null rather than as a measurement
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what this limits: reading the recurrent loop as observed rather than as the simplest account of an absence
limitations[9]1.0the tagger's words
transfersJOINT PERI-EVENT CANONICAL CORRELATION (jPECC) ANALYSIS, A NOVEL EXTENSION OF THE “joint Peristimulus Time Histogram” METHOD MODIFIED TO DETECT CORRELATIONS IN A “communication subspace” BETWEEN TWO POPULATIONS
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
transfers[0]1.0the tagger's words
transfersa version of CHOICE PROBABILITY ANALYSIS FOR TASKS WITH MANY STIMULUS CONDITIONS, CALLED COMBINED-CONDITIONS CHOICE PROBABILITY, which QUANTIFIES THE PROBABILITY THAT A NEURON'S SPIKE COUNT WILL BE GREATER ON TRIALS WITH ONE CHOICE THAN TRIALS OF ANOTHER, FOR MATCHED STIMULUS CONDITIONS
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transfers[1]1.0the tagger's words
controlsthe visual contrast matched between the conditions being compared
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the activity difference reflecting different visual drive - CONTRALATERAL VISUAL STIMULUS CONTRASTS WERE MATCHED so that DIFFERENCES IN ACTIVITY DO NOT REFLECT DIFFERING VISUAL DRIVE · outcome (stated by the tagger, no quotation): held
controls[0]0.7the tagger's words
controlsthe task-context comparison restricted to trials where the animal did nothing, against passive presentation
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eliminates: movement explaining the context difference - BOTH VISUAL STIMULI AND BEHAVIORAL REPORTS WERE IDENTICAL, and the conditions were MATCHED FOR VISUAL STIMULATION AND (LACK OF) ACTION · outcome (stated by the tagger, no quotation): held
controls[1]1.0the tagger's words
controlsthe engagement index computed from PRE-STIMULUS activity only
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the index being a movement correlate - WE EXAMINED ONLY PRE-STIMULUS ACTIVITY, WHICH COULD NOT BE CONFLATED WITH THE LARGE NON-SPECIFIC RESPONSES RELATED TO MOVEMENTS · outcome (stated by the tagger, no quotation): held
controls[2]1.0the tagger's words
controlsthe engagement effect tested against pupil diameter, video-detectable movement, previous reward and inter-trial interval
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: arousal, movement, reward history and timing - the effect COULD NOT BE FULLY EXPLAINED BY VARIABILITY IN PUPIL DIAMETER, IN OVERT MOVEMENTS DETECTABLE BY VIDEO RECORDINGS, IN THE PRESENCE OF A REWARD ON THE PREVIOUS TRIAL, OR IN THE INTER-TRIAL INTERVAL · outcome (stated by the tagger, no quotation): held
controls[3]1.0the tagger's words
controlsthe kernel test's threshold set from shuffled data
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the encoding counts being a product of the test - WE USED PARAMETERS WHICH GAVE FALSE-POSITIVE ERROR RATES OF 0.33% ON SHUFFLED DATA · outcome (stated by the tagger, no quotation): held
controls[4]1.0the tagger's words
controlsthe whole choice result repeated with a second, independent statistic
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the conclusion depending on the kernel model - a version of CHOICE PROBABILITY ANALYSIS FOR TASKS WITH MANY STIMULUS CONDITIONS was developed and EMPLOYING THIS METHOD, WE OBTAINED SIMILAR RESULTS · outcome (stated by the tagger, no quotation): held
controls[5]1.0the tagger's words
controlsthe analysis restricted to activity before the movement
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: activity caused by the movement being read as predicting it - AS OUR QUESTION CONCERNS ACTIVITY PREDICTIVE OF UPCOMING MOVEMENTS, WE APPLIED THIS ANALYSIS ONLY TO PRE-MOVEMENT ACTIVITY · outcome (stated by the tagger, no quotation): held
controls[6]1.0the tagger's words
sensesA CRITERION FOR WHAT COUNTS AS EVIDENCE, STATED BEFORE ANYTHING IS MEASURED: NEURONAL SIGNALS THAT CORRELATE WITH ACTION DO NOT NECESSARILY CORRELATE WITH ACTION SELECTION - TO CARRY SUCH CHOICE-RELATED SIGNALS, A BRAIN REGION MUST CONTAIN NEURONS WHOSE FIRING SELECTIVELY PREDICTS THE CHOSEN ACTION BEFORE THE ACTION OCCURS
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senses[0]1.0the tagger's words
sensesAND A WHOLE CLASS OF DESIGNS CANNOT MEET IT: GO/NOGO TASKS CANNOT DISTINGUISH NEURONS THAT NONSPECIFICALLY FIRE FOR ANY ACTION, FROM NEURONS SELECTIVE FOR SPECIFIC CHOICES. Not a result being corrected - a design being retired, and every finding that used it inherits the ambiguity
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senses[1]1.0the tagger's words
sensesTHE SAME STIMULUS AND THE SAME behavior, DIFFERENT ACTIVITY: BOTH VISUAL STIMULI AND BEHAVIORAL REPORTS WERE IDENTICAL, and EVEN THOUGH THE TWO CONDITIONS WERE MATCHED FOR VISUAL STIMULATION AND (LACK OF) ACTION, THEY WERE ACCOMPANIED IN MANY AREAS BY DIFFERENT ACTIVITY, BOTH BEFORE AND AFTER STIMULUS PRESENTATION. The response is not a property of the stimulus
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senses[2]1.0the tagger's words
sensesand the context effect has OPPOSITE SIGNS in different structures: ACTIVITY IN VISp WAS LOWER IN THE TASK THAN IN THE PASSIVE TRIALS, WHEREAS ACTIVITY IN CP SHOWED THE OPPOSITE MODULATION - WHILE NEOCORTEX AND SENSORY THALAMUS SHOWED A NET DECREASE, OTHER REGIONS SHOWED A CONSISTENT INCREASE. A brain-wide average of this is zero
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senses[3]1.0the tagger's words
sensesTHE GLOBAL SIGNAL IS ABOUT MOVING, NOT ABOUT THE TASK: THE WIDELY DISTRIBUTED ACTIVITY SEEN FOLLOWING TRIAL ONSET WAS THEREFORE PRESENT ONLY WHEN ANIMALS MOVED, AND REGARDLESS OF THE PARTICULAR STIMULUS AND PARTICULAR ACTION
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senses[4]1.0the tagger's words
sensesand the ordering of areas reverses with the side of the stimulus: WHEN THE MOUSE SUCCESSFULLY SELECTED AN IPSILATERAL STIMULUS, MOST AREAS WERE AGAIN ACTIVATED, BUT VIS AND SCs WERE NOW AMONGST THE LAST AREAS TO RESPOND, RATHER THAN THE FIRST
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senses[5]1.0the tagger's words
sensesWHAT IS GLOBAL AND WHAT IS NOT, MEASURED RATHER THAN ASSERTED: NEURONS ENCODING ACTION WERE SPREAD THROUGHOUT ALL RECORDED REGIONS, and THE GREAT MAJORITY OF NEURONS ENCODING ACTION DID NOT REQUIRE AN ADDITIONAL CHOICE KERNEL - THEY RESPONDED EQUALLY FOR MOVEMENTS IN EITHER DIRECTION
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senses[6]1.0the tagger's words
sensesand the negative that makes the positive mean something: CHOICE-SELECTIVE NEURONS WERE NOT FOUND IN VISp, although THIS SET OF REGIONS ENCODING CHOICE OVERLAPPED PARTIALLY WITH THE VISUAL PATHWAY
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senses[7]1.0the tagger's words
sensesTHE SAME VARIABLE ENCODED IN TWO INCOMPATIBLE WAYS IN TWO PLACES: IN MIDBRAIN NEARLY ALL CHOICE-SELECTIVE NEURONS (53/54, 98%) PREFERRED CONTRALATERAL CHOICES, whereas in forebrain A SIZEABLE PROPORTION PREFERRED IPSILATERAL CHOICES (19/48, 40%). A `midbrain encodes choice` tag and a `forebrain encodes choice` tag are the same words for opposite arrangements
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senses[8]1.0the tagger's words
sensesA NULL DOING THE ARGUMENTATIVE WORK: WE COULD NOT DISTINGUISH THE TIMING OF CHOICE-RELATED SIGNALS BETWEEN THESE REGIONS, AN OBSERVATION PARSIMONIOUSLY EXPLAINED BY A RECURRENT LOOP ACROSS THEM - the loop is the simplest account of an absence, and is labeled as such
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senses[9]1.0the tagger's words
sensesand the null was sought two ways: the decoding time course COULD NOT BE STATISTICALLY DISTINGUISHED BETWEEN CHOICE-SELECTIVE REGIONS, and jPECC REVEALED NO LAG FOR ACTIVITY CORRELATIONS BETWEEN FRONTAL AND MIDBRAIN AREAS while it DID reveal A CONSISTENT TIME-LAG between visual and frontal cortex
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senses[10]1.0the tagger's words
sensesTHE MODEL EXPLAINS LITTLE OF WHAT IT PREDICTS WELL: THE FRACTION OF CROSS-VALIDATED VARIANCE THE KERNELS EXPLAINED WAS FREQUENTLY SMALL, EVEN FOR NEURONS WHOSE MEAN RATES THEY ACCURATELY PREDICTED - 50.2% for one example neuron and 13.6% for another
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senses[11]1.0the tagger's words
sensesTHE ERROR RATE OF THE CLASSIFICATION IS PRINTED: WE USED PARAMETERS WHICH GAVE FALSE-POSITIVE ERROR RATES OF 0.33% ON SHUFFLED DATA - so every count of encoding neurons in this paper has a stated denominator of error
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senses[12]1.0the tagger's words
sensesAN INDEX DEFINED BY THE DIFFERENCE BETWEEN TWO CONTEXTS, AND CHECKED AGAINST FOUR CONFOUNDS: the engagement index COULD NOT BE FULLY EXPLAINED BY VARIABILITY IN PUPIL DIAMETER, IN OVERT MOVEMENTS DETECTABLE BY VIDEO RECORDINGS, IN THE PRESENCE OF A REWARD ON THE PREVIOUS TRIAL, OR IN THE INTER-TRIAL INTERVAL
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senses[13]1.0the tagger's words
sensesENGAGEMENT MOVES CORTEX AND SUBCORTEX IN OPPOSITE DIRECTIONS: CORRELATES OF ENGAGEMENT ARE CHARACTERIZED BY ENHANCED SUBCORTICAL ACTIVITY AND SUPPRESSED NEOCORTICAL ACTIVITY PRIOR TO VISUAL STIMULUS ONSET - and the authors flag it, ENGAGEMENT-RELATED CORTICAL SUPPRESSION MIGHT SEEM SURPRISING, GIVEN THAT VISUAL CORTEX IS REQUIRED FOR PERFORMANCE OF THIS TASK
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senses[14]1.0the tagger's words
sensesA QUARTER OF THE DATA HAS NO ADDRESS: WE RECORDED FROM 29,134 NEURONS, OF WHICH 22,458 WERE LOCALIZABLE TO ONE OF 42 BRAIN REGIONS - every per-region number in the paper has that denominator behind it
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senses[15]1.0the tagger's words
sensesand a majority are modulated, in both directions: A SIZEABLE FRACTION OF ALL NEURONS (60.0%, 13,466 NEURONS) HAD SIGNIFICANT MODULATION OF FIRING RATE DURING THE TASK - MOST OF THESE NEURONS (74.3%) CONSISTENTLY INCREASED THEIR ACTIVITY, BUT A SIZEABLE MINORITY (20.2%) CONSISTENTLY DECREASED
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senses[16]1.0the tagger's words
sensesWHAT THE GLOBAL SIGNAL CANNOT BE, ON A TIMING ARGUMENT: THESE SIGNALS MAY COMPRISE FORMS OF COROLLARY DISCHARGE, BUT CANNOT REFLECT SENSORY RE-AFFERENCE AS THEY WERE OBSERVED PRIOR TO MOVEMENT ONSET
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senses[17]1.0the tagger's words
sensesand the finding may belong to the trained animal rather than to the structure: WHETHER VISUAL NEURONS WOULD BE FOUND these ‘motor’ AREAS IN UNTRAINED ANIMALS IS NOT CLEAR FROM THESE DATA
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senses[18]1.0the tagger's words
alternativesclaim_type: existence
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a second reading reaching the same value. Recorded: existence — note: a second reading reaching the same value from a different sentence. Not applied - a person decides.
alternatives.claim_typethe tagger's words
alternativesmethod: fit each neuron with kernels for vision, action and choice, then ask by a nested cross-validated test whether the kernel under test is REQUIRED, with a declared false-positive rate on shuffled data
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a second reading DIFFERING from the recorded value. Recorded: electrophysiology — note: a second reading, verbatim-verified, disagreeing with the value on the record. Not applied - a person decides.
alternatives.methodthe tagger's words
alternativesphenomenon: activity that appears everywhere in the brain before a movement, in regions with no established role in choosing it
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a second reading DIFFERING from the recorded value. Recorded: brain-wide distribution of neural coding for vision, action, choice and task engagement — 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 → Guo et al (ref. 45), headplate and recording-chamber implantation method
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claim_relations[0]the tagger's words
claim_relationsbuilds-on → Treves and Rolls (ref. 54), sparseness measure, adapted here as the Focality Index
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claim_relations[1]the tagger's words
claim_relationsextends → The "joint Peristimulus Time Histogram" method (refs 35, 36), extended here to jPECC
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claim_relations[2]the tagger's words
claim_relationsbuilds-on → The previously described two-alternative unforced choice task (ref. 3)
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claim_relations[3]the tagger's words
claim_relationscritiques → go/nogo designs as evidence about choice-selective neurons
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differs in: what the design can separate - GO/NOGO TASKS CANNOT DISTINGUISH NEURONS THAT NONSPECIFICALLY FIRE FOR ANY ACTION, FROM NEURONS SELECTIVE FOR SPECIFIC CHOICES
claim_relations[4]1.0the tagger's words
claim_relationsextends → reports of widespread action correlates in multiple species
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claim_relations[5]0.6the tagger's words
claim_relationsqualifies → the classical set of choice-related areas (frontal cortex, striatum, SNr, deep superior colliculus)
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differs in: two regions nobody expected - BUT ALSO UNEXPECTED REGIONS INCLUDING THE MIDBRAIN RETICULAR NUCLEUS AND ZONA INCERTA
claim_relations[6]0.8the tagger's words
concept_edgesaction —distinct-from→ choice
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strength of the relation: 1 · note: NEURONAL SIGNALS THAT CORRELATE WITH ACTION DO NOT NECESSARILY CORRELATE WITH ACTION SELECTION
also in: action · choice
concept_edges[0]1.0the tagger's words
concept_edgesgo/nogo —contrasted-with→ choice
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strength of the relation: 1 · note: GO/NOGO TASKS CANNOT DISTINGUISH NEURONS THAT NONSPECIFICALLY FIRE FOR ANY ACTION, FROM NEURONS SELECTIVE FOR SPECIFIC CHOICES Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the span argues for multi-alternative over go/no-go tasks; contrasted-with is loose.
also in: go/nogo · choice
concept_edges[2]1.0the tagger's words
concept_edgesmidbrain —contrasted-with→ forebrain
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differs in: THE AXIS IS WHAT THEY SHARE AND WHAT THEY DO NOT, BOTH NAMED IN ONE CLAUSE. 'Although Quotation withheld.' Identical on timing, different on code. A bare 'contrasted-with' records the difference and drops the fact that the obvious explanation - one region leading the other - is ruled out in the same sentence. · strength of the relation: 1 · note: ALTHOUGH Quotation withheld - a 'BILATERAL' ENCODING OF BOTH CHOICES IN THE FOREBRAIN, VERSUS a 'UNILATERAL' ENCODING OF CONTRALATERAL CHOICES IN THE MIDBRAIN 2026-08-20 the project re-read worst chars/edge queue): SOUND - the passage is built as this contrast and says so twice - 'By contrast' and 'in the forebrain…'. Both endpoints named, type correct. KEEP.
also in: midbrain · forebrain
concept_edges[9]1.0the tagger's words
concept_edgespassive —contrasted-with→ Miss
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strength of the relation: 1 · note: BOTH VISUAL STIMULI AND BEHAVIORAL REPORTS WERE IDENTICAL, and yet THEY WERE ACCOMPANIED IN MANY AREAS BY DIFFERENT ACTIVITY, BOTH BEFORE AND AFTER STIMULUS PRESENTATION
also in: passive · Miss
concept_edges[11]1.0the tagger's words
content_tagsANOVA
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also in: ANOVA
content_tags.statistics[0]the tagger's words
content_tagsANOVA
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also in: ANOVA
content_tags.statistics[1]the tagger's words
content_tagsnested ANOVA
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also in: nested ANOVA
content_tags.statistics[2]the tagger's words
content_tagschi-squared test
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content_tags.statistics[3]the tagger's words
content_tagst-test
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also in: t-test
content_tags.statistics[4]the tagger's words
content_tagsBonferroni correction
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content_tags.statistics[5]the tagger's words
content_tagscross-validation
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content_tags.statistics[6]the tagger's words
content_tagsregression
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also in: regression
content_tags.statistics[7]the tagger's words
content_tagslogistic regression
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content_tags.statistics[8]the tagger's words
content_tagsgeneralized linear model
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content_tags.statistics[9]the tagger's words
content_tagsbootstrap
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also in: bootstrap
content_tags.statistics[10]the tagger's words
content_tagsprincipal component analysis
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content_tags.statistics[11]the tagger's words
content_tagscanonical correlation analysis
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content_tags.statistics[12]the tagger's words
content_tagsROC / Mann-Whitney U statistic
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content_tags.statistics[13]the tagger's words
content_tagspermutation test
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content_tags.statistics[14]the tagger's words
content_tagstwo-way ANOVA
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also in: two-way ANOVA
content_tags.statistics[15]1.0the tagger's words
content_tagsFisher's exact test
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content_tags.statistics[16]1.0the tagger's words
content_tagscross-validated
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content_tags.statistics[17]1.0the tagger's words
content_tagsNeurons whose firing rose non-specifically at the moment of action initiation were present in nearly every one of the 42 recorded brain regions.
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content_tags.findings[0]the tagger's words
content_tagsNeurons coding the visual stimulus and the upcoming choice were not brain-wide but restricted to particular neocortical, basal ganglia and midbrain regions.
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content_tags.findings[1]the tagger's words
content_tagsMidbrain choice neurons were almost all activated before contralateral turns and suppressed before ipsilateral ones, whereas forebrain choice neurons could prefer either direction.
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content_tags.findings[2]the tagger's words
content_tagsPre-stimulus activity across the brain predicted whether the mouse would respond on a given trial, with subcortical activity raised and neocortical activity lowered during engagement.
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content_tags.findings[3]the tagger's words
content_tagsTHE TIME COURSE OF CHOICE DECODING COULD NOT BE STATISTICALLY DISTINGUISHED BETWEEN CHOICE-SELECTIVE REGIONS IN FRONTAL CORTEX, STRIATUM, AND MIDBRAIN
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content_tags.findings[4]the tagger's words
content_tagsChoice-selective neurons were found in frontal cortex, striatum, substantia nigra pars reticulata, higher-order thalamus and deep superior colliculus, and unexpectedly also in the midbrain reticular nucleus and zona incerta.
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content_tags.findings[5]the tagger's words
content_tagsOn trials where the mouse missed a contralateral stimulus and did not act, activity appeared in a visual pathway of visual areas, basal ganglia and midbrain but failed to propagate globally.
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content_tags.findings[6]the tagger's words
content_tagsSixty per cent of all recorded neurons (13,466) showed significant task-related firing-rate modulation.
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content_tags.findings[7]the tagger's words
content_tagsCanonical-correlation analysis of simultaneous populations showed visual cortex leading frontal cortex and midbrain, but no lead-lag relationship at all between frontal cortex and midbrain.
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content_tags.findings[8]the tagger's words
content_tagsThe engagement index separated Go from Miss trials consistently across recordings, an effect not fully explained by pupil diameter, overt movement, previous reward or inter-trial interval.
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content_tags.findings[9]the tagger's words
content_tagsMore than half of midbrain choice-selective neurons increased firing before one choice and fell below baseline before the other.
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content_tags.findings[10]the tagger's words
content_tagsNEURONS ENCODING ACTION WERE SPREAD THROUGHOUT ALL RECORDED REGIONS, and THE GREAT MAJORITY DID NOT REQUIRE AN ADDITIONAL CHOICE KERNEL - THEY RESPONDED EQUALLY FOR MOVEMENTS IN EITHER DIRECTION
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content_tags.findings[11]1.0the tagger's words
content_tagsCHOICE-SELECTIVE NEURONS WERE NOT FOUND IN VISp, and were found in TWO SUBCORTICAL NUCLEI WHICH UNEXPECTEDLY CONTAINED NEURONS SELECTIVE FOR CHOICE (MRN AND ZI)
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content_tags.findings[12]1.0the tagger's words
content_tagsIN MIDBRAIN NEARLY ALL CHOICE-SELECTIVE NEURONS (53/54, 98%) PREFERRED CONTRALATERAL CHOICES, while in forebrain A SIZEABLE PROPORTION PREFERRED IPSILATERAL CHOICES (19/48, 40%)
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content_tags.findings[13]1.0the tagger's words
content_tagsTHE WIDELY DISTRIBUTED ACTIVITY SEEN FOLLOWING TRIAL ONSET WAS PRESENT ONLY WHEN ANIMALS MOVED, AND REGARDLESS OF THE PARTICULAR STIMULUS AND PARTICULAR ACTION
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content_tags.findings[14]1.0the tagger's words
content_tagsEVEN THOUGH THE TWO CONDITIONS WERE MATCHED FOR VISUAL STIMULATION AND (LACK OF) ACTION, THEY WERE ACCOMPANIED IN MANY AREAS BY DIFFERENT ACTIVITY, BOTH BEFORE AND AFTER STIMULUS PRESENTATION
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content_tags.findings[15]1.0the tagger's words
content_tagsWHILE NEOCORTEX AND SENSORY THALAMUS SHOWED A NET DECREASE IN PRE-STIMULUS ACTIVITY DURING TASK CONTEXT, OTHER REGIONS SHOWED A CONSISTENT INCREASE
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content_tags.findings[16]1.0the tagger's words
content_tagsthe time course of choice decoding COULD NOT BE STATISTICALLY DISTINGUISHED BETWEEN CHOICE-SELECTIVE REGIONS IN FRONTAL CORTEX, STRIATUM, AND MIDBRAIN
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content_tags.findings[17]1.0the tagger's words
content_tagsWE RECORDED FROM 29,134 NEURONS, OF WHICH 22,458 WERE LOCALIZABLE TO ONE OF 42 BRAIN REGIONS
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content_tags.findings[18]1.0the tagger's words
content_tagsA SIZEABLE FRACTION OF ALL NEURONS (60.0%, 13,466 NEURONS) HAD SIGNIFICANT MODULATION OF FIRING RATE DURING THE TASK - 74.3% CONSISTENTLY INCREASED, 20.2% CONSISTENTLY DECREASED
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content_tags.findings[19]1.0the tagger's words
content_tagsTHE FRACTION OF CROSS-VALIDATED VARIANCE THE KERNELS EXPLAINED WAS FREQUENTLY SMALL, EVEN FOR NEURONS WHOSE MEAN RATES THEY ACCURATELY PREDICTED
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content_tags.findings[20]1.0the tagger's words
content_tagschoice
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also in: choice
content_tags.definitions[0]the tagger's words
content_tagschoice-related signal
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content_tags.definitions[1]the tagger's words
content_tagscombined-conditions Choice Probability (ccCP)
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content_tags.definitions[3]the tagger's words
content_tagsjoint Peri-Event Canonical Correlation (jPECC)
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content_tags.definitions[4]the tagger's words
content_tagsengagement index
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content_tags.definitions[5]the tagger's words
content_tagsFocality index
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content_tags.definitions[6]the tagger's words
content_tagsa statistic that QUANTIFIES THE PROBABILITY THAT A NEURON'S SPIKE COUNT WILL BE GREATER ON TRIALS WITH ONE CHOICE THAN TRIALS OF ANOTHER, FOR MATCHED STIMULUS CONDITIONS, JUST AS IN CLASSIC CHOICE PROBABILITY
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content_tags.definitions[7]1.0the tagger's words
content_tags‘Action’ kernel
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content_tags.definitions[8]the tagger's words
content_tags‘Choice’ kernel
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content_tags.definitions[9]the tagger's words
content_tagscontrast condition
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content_tags.variables[0]the tagger's words
content_tagsfiring rate
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also in: firing rate
content_tags.variables[2]the tagger's words
content_tagscontralateral visual stimulus contrast
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content_tags.variables[4]the tagger's words
content_tagschoice
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also in: choice
content_tags.variables[6]1.0the tagger's words
content_tagsengagement
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also in: engagement
content_tags.variables[7]1.0the tagger's words
content_tagspupil area
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also in: pupil area
content_tags.variables[8]the tagger's words
content_tagsmotion energy
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also in: motion energy
content_tags.variables[9]the tagger's words
content_tagsprevious trial reward outcome
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content_tags.variables[10]the tagger's words
content_tagsinter-trial interval
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content_tags.variables[11]the tagger's words
content_tags29,134 — neurons recorded in total, of which 22,458 could be assigned to one of 42 brain regions
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content_tags.quantities[0]the tagger's words
content_tags60.0% — share of recorded neurons with significant task-related firing-rate modulation
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content_tags.quantities[1]the tagger's words
content_tags53/54, 98% — proportion of midbrain choice-selective neurons preferring contralateral choices
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content_tags.quantities[2]the tagger's words
content_tags19/48, 40% — proportion of forebrain choice-selective neurons preferring ipsilateral choices, significantly more than in midbrain
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content_tags.quantities[3]the tagger's words
content_tags0.33% — false-positive rate of the kernel selectivity test estimated on shuffled data
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content_tags.quantities[4]the tagger's words
content_tags0.079 / 0.069 / 0.040 — THIS FOCALITY INDEX WAS 0.079 FOR CHOICE, 0.069 FOR VISUAL KERNELS AND 0.040 FOR ACTION KERNELS - the differences between Choice and Move, and between Contralateral Vision and Action, WERE STATISTICALLY SIGNIFICANT
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content_tags.quantities[5]the tagger's words
content_tags1.7 ± 2.5% — incorrect-choice rate on high-contrast single-stimulus trials, with 10.1% misses
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content_tags.quantities[6]the tagger's words
content_tags94.1% ± 0.6% — proportion of passive-replay trials with high-contrast stimuli in which the mouse made no wheel movement
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content_tags.quantities[7]the tagger's words
content_tags88.7 μm — median absolute error of the longitudinal probe-to-atlas alignment, close to the 70 micrometer probe shank width
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content_tags.quantities[8]the tagger's words
content_tags29/54, 54% — midbrain choice-selective neurons showing directionally opposed activity (enhanced for one choice, suppressed below baseline for the other)
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content_tags.quantities[9]the tagger's words
content_tags53/54, 98% — midbrain choice-selective neurons preferring contralateral choices
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depends on: the structure - the matched forebrain figure is 19/48, 40% PREFERRING IPSILATERAL CHOICES
content_tags.quantities[10]1.0the tagger's words
content_tags0.33% — the FALSE-POSITIVE ERROR RATE ON SHUFFLED DATA that the kernel test's parameters were set to give
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content_tags.quantities[11]1.0the tagger's words
content_tags29,134 — neurons recorded, OF WHICH 22,458 WERE LOCALIZABLE TO ONE OF 42 BRAIN REGIONS
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content_tags.quantities[12]1.0the tagger's words
content_tags60.0%, 13,466 neurons — the fraction with SIGNIFICANT MODULATION OF FIRING RATE DURING THE TASK
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content_tags.quantities[13]1.0the tagger's words
content_tags50.2% ... 13.6% — cross-validated variance explained for two example neurons whose mean rates the model predicted accurately
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content_tags.quantities[14]1.0the tagger's words

Interpretive choices

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© 2026 Shir Sivroni · ORCID 0009-0000-2597-2824