Neural Networks of the Mouse Neocortex

Zingg, Hintiryan, Gou, Song, Bay, Bienkowski, Foster, Yamashita · Cell · 2014 · neuroscience · 10.1016/j.cell.2014.02.023 · record Zingg2014-neural-networks-of-the-mouse-neocortex
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. The underlying technique is anterograde/retrograde tract tracing in mice, which the method vocabulary cannot express; 'system-or-tool-building' was chosen because the paper's stated deliverable is a resource (the iConnectome atlas, matrices and interactive cortical map). Claim type is 'existence' for the subnetwork organisation finding rather than 'method' for the resource, since the abstract's headline is the discovered eight-subnetwork architecture. The paper reports internal cross-validation (89% agreement between anterograde and retrograde labelling) but no external replication, so replication status stays untested. 2026-08-12, 2026-08-15 and 2026-08-25 schema-0.3 passes: every quote verified as an exact substring of the staged text and anchored at merge time; concept terms verified present; every edge endpoint an existing node.
How to read this page. The article itself is not reproduced here — this paper is not cleared for redistribution, so what follows is the tag layer alone. The evidence sentences are withheld with the article. The table at the foot lists every tag the record carries; each row names the facet it belongs to, and the whose words column says whether the tag records the paper's own wording or the tagger's sentence about the paper. Every tag links to each other paper in the corpus carrying it. The machine-readable edition of the same thing is the TEI file beside this one, where the tags live in standOff, and the article is at its publisher via the link below. 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 WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below.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.
Other fields define these differently the same word, defined another way in another discipline
clustering 3 fields

Tags on this paper

Every tag the record carries, each linking to every other paper in the corpus that carries it. A tag appears here whether or not its words occur in the article — the spans below are only the ones a sentence in this paper licenses. Of the 21 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.
connectome cortical connectivity atlas subnetworks connectivity matrices double co-injection anterograde retrograde hubs clustering algorithm somatic sensorimotor medial lateral claustrum lateral entorhinal area prefrontal cortex cross-modal modulation laminar specificity meso-connectome iConnectome semi-quantitative trisynaptic circuit tract tracing neocortex retrosplenial insular perirhinal macro- or meso-connectome hub clustering intraconnectivity interconnectivity injection site density of intraconnectivity laminar distribution patterns anterograde and retrograde labeling cluster analysis percentage agreement between two methods weighted directional connectivity matrices semi-quantitative densities system-or-tool-building

Legend

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/10.1016/j.cell.2014.02.023. The reading view exists for the papers whose licence permits it.

Every tag on this page

alternatives 3 · claim_relations 10 · claim_type 1 · concept_edges 4 · content_tags 53 · contribution 1 · controls 1 · limitations 9 · mechanisms 11 · method 1 · object_of_study 1 · phenomenon 1 · research_question 1 · senses 6 · 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_studyhow areas across the entire mouse neocortex organise into communication networks, mapped by over 600 traced pathways
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object_of_studythe paper's words
research_questionhow do different cortical areas communicate at the network level across the whole structure
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research_questionthe paper's words
contributiondelivers a cortical connectivity atlas and matrices from uniformly collected tracer data, and finds the neocortex clusters into four somatic sensorimotor, two medial and two lateral subnetworks
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contributionthe paper's words
claim_typeexistence
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claim_typethe paper's words
phenomenoncortico-cortical connectivity of the mouse neocortex
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phenomenonthe paper's words
methodsystem-or-tool-building
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methodthe paper's words
mechanismseach injection is designed to return four kinds of information at once - inputs, outputs, reciprocal connections and intermediate stations - by pairing an anterograde with a retrograde tracer
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mechanisms[0]1.0the tagger's words
mechanismsthe two tracer directions are used as independent measurements of the same connection, and their agreement is reported as a validity check
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mechanisms[1]1.0the tagger's words
mechanismsinjection specificity is cross-validated by tracing the reverse direction: retrograde tracer into the regions the anterograde labelling had targeted
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mechanisms[2]1.0the tagger's words
mechanismsthe subnetworks are not stipulated but produced by reordering the matrix with a clustering algorithm, and named afterwards
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mechanisms[3]1.0the tagger's words
mechanismsthe clustering makes the matrix diagonal readable as within-subnetwork density and the off-diagonal as between-subnetwork traffic
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mechanisms[4]1.0the tagger's words
mechanismsthe whole analysis rests on hand annotation, because no tool can identify fine anatomic boundaries, and the strengths recorded are semi-quantitative
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mechanisms[5]1.0the tagger's words
mechanismseach pathway is rendered as a separate layer in a common anatomic frame so that arbitrary combinations can be viewed together
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mechanisms[6]1.0the tagger's words
mechanismsuniform collection and analysis is claimed as the advantage over connectivity matrices assembled from published literature
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mechanisms[7]1.0the tagger's words
mechanismsthe somatosensory subdivisions used as network nodes are themselves validated against known somatotopy in the brainstem before being used
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mechanisms[8]0.8the tagger's words
mechanismsa visualisation artefact is disclosed rather than left for the reader to discover: the injection sites look larger than they are once the image is brightened enough to show fine fibers
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mechanisms[9]1.0the tagger's words
mechanismsthe resource is framed as the input to later causal work, naming the specific techniques that would test any mapped pathway
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mechanisms[10]0.95the tagger's words
limitationsInterpreting large-scale connectivity data remains an unsolved challenge.
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what this limits: the interpretive claims, not the resource: the paper demonstrates THE FEASIBILITY OF PRODUCING AND COLLECTING LARGE-SCALE CONNECTIVITY DATA, and names interpretation as the unsolved part
limitations[0]the tagger's words
limitationsPublished injection-site images overstate the true injection size.
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what this limits: any reading of injection extent from the published figures: WHEN IMAGES ARE ADJUSTED TO REVEAL FINE FIBERS, INJECTION [extent appears larger] than the ~250-500um stated
limitations[1]the tagger's words
limitationsAnnotation had to be done by hand because no automated tool can delineate fine anatomical boundaries.
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what this limits: the precision of every areal boundary in the atlas: INFORMATICS TOOLS THAT AUTOMATICALLY AND PRECISELY IDENTIFY FINE ANATOMIC BOUNDARIES ... ARE NON-EXISTENT, so annotation is by hand
limitations[2]the tagger's words
limitationsThe mapped long-range interactions have not been validated at the synaptic or cell-type level.
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what this limits: the synaptic and cell-type reading of any mapped connection: these MAY BE VALIDATED AT THE SYNAPTIC LEVEL USING TRANSSYNAPTIC VIRAL TRACING - not done here
limitations[3]the tagger's words
limitationsinterpreting connectivity data at this scale is named as the unsolved part, not the collection of it
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what this limits: the same scope as limitations[0] - collection is demonstrated, interpretation is not
limitations[4]1.0the tagger's words
limitationsno automated tool exists for the annotation step, so the atlas is hand-made and semi-quantitative
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what this limits: the same scope as limitations[2], with the consequence: the analysis is hand-made and semi-quantitative
limitations[5]1.0the tagger's words
limitationsthe matrices discard route, laminar specificity and topography, which the authors call critical features of networks
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what this limits: every use of the connectivity matrices: THEY EXCLUDE DETAILS LIKE PROJECTIONS ROUTES, LAMINAR SPECIFICITY OF PROJECTIONS, OR TOPOGRAPHICAL organisation - the condensed view drops features the authors call critical
limitations[6]1.0the tagger's words
limitationsthe mapped connections are anatomical and require separate validation at the synaptic and functional level
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what this limits: the same scope as limitations[3] - anatomical connections, awaiting synaptic and functional validation
limitations[7]1.0the tagger's words
limitationshuman network findings are held to need validation in animal models at higher resolution, which is the gap this atlas is built to fill
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what this limits: the transfer of human network findings: IT IS NECESSARY TO VALIDATE THESE NETWORKS USING RELIABLE NEURAL TRACT TRACING METHODS IN ANIMAL MODELS AT A HIGHER RESOLUTION
limitations[8]0.9the tagger's words
transfersthe hub - a region of high network interaction - imported to interpret the claustrum and lateral entorhinal area
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transfers[0]0.95the tagger's words
transfersreordering nodes so that dense groups fall along the diagonal, which converts a connectivity table into a set of named subnetworks
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transfers[1]0.95the tagger's words
controlscross-validating anterograde injection specificity by applying retrograde tracers to the regions targeted by anterogradely labelled axon terminals, and the reverse
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eliminates: that the anterograde labelling reflects nonspecific injection spread rather than a genuine projection · outcome: held
controls[0]0.85the tagger's words
sensesconnectome - as the C. elegans-style complete synaptic wiring diagram versus as the meso-scale regional map this paper builds
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senses[0]0.95the tagger's words
sensescortical network - as derived from human fMRI and diffusion imaging versus as traced anatomically in an animal model; the paper treats the second as validation of the first
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senses[1]1.0the tagger's words
sensesconnectivity matrix - assembled piecemeal from published literature versus collected and analysed uniformly; the paper claims the difference matters
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senses[2]1.0the tagger's words
sensessubnetwork - as a cluster in a reordered matrix versus as an anatomically or functionally defined system; here the first produces the second, and the names come last
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senses[3]1.0the tagger's words
sensesprimary sensory cortex as strictly unisensory versus as cross-modally modulated - a boundary the connectivity data is said to challenge
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senses[4]1.0the tagger's words
sensesconnection strength - as a semi-quantitative hand-graded density, which is what the weights in every matrix here actually are
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senses[5]1.0the tagger's words
alternativesclaim_type: method
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a second reading DIFFERING from the recorded value. Recorded: existence — note: a second reading, verbatim-verified, disagreeing with the value on the record. Not applied - a person decides.
alternatives.claim_typethe tagger's words
alternativesmethod: double co-injection tract tracing, one anterograde and one retrograde tracer per site, across the whole neocortex, hand-annotated into weighted directional matrices and clustered
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a second reading DIFFERING from the recorded value. Recorded: system-or-tool-building — note: a second reading, verbatim-verified, disagreeing with the value on the record. Not applied - a person decides.
alternatives.methodthe tagger's words
alternativesphenomenon: large-scale cortico-cortical network organisation
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a second reading DIFFERING from the recorded value. Recorded: cortico-cortical connectivity of the mouse neocortex — 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 → the double co-injection tract tracing method of Thompson and Swanson (2010)
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claim_relations[0]the tagger's words
claim_relationsextends → cortical connectivity matrices previously assembled from literature data (Honey et al., 2007; Sporns et al., 2007; Markov et al., 2010)
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claim_relations[1]the tagger's words
claim_relationsbuilds-on → the concept of cross-modal modulation (Driver and Noesselt, 2008; Stein and Stanford, 2008)
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claim_relations[2]the tagger's words
claim_relationsextends → the account of the lateral entorhinal cortex as a gateway to the hippocampus (de Curtis and Paré, 2004)
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claim_relations[3]the tagger's words
claim_relationsbuilds-on → the experimental procedures of Hintiryan et al. (2012)
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claim_relations[4]the tagger's words
claim_relationscritiques → cortical connectivity matrices assembled piecemeal from the published literature
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differs in: THE AXIS IS HOW THE DATA WERE ASSEMBLED. 'the networks reported here are based on data collected and analyzed in a homogenous fashion rather than gathered piecemeal from the literature.' A critique of provenance rather than of any result - and one this project should read against itself, since a cross-field corpus is assembled exactly the way this sentence criticises.
claim_relations[5]1.0the tagger's words
claim_relationsextends → human structural and functional network studies using fMRI and diffusion tensor imaging, which the paper holds need animal validation at higher resolution
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claim_relations[6]1.0the tagger's words
claim_relationscontradicts → the assumption that mammalian primary sensory cortices are strictly unisensory
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claim_relations[7]0.95the tagger's words
claim_relationsbuilds-on → the network-science framing of brain organisation, including the hub concept
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claim_relations[8]0.95the tagger's words
claim_relationsextends → wiring diagrams previously assembled only for specific functional systems or smaller scales
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claim_relations[9]0.95the tagger's words
concept_edgessubnetworks —operationalised-as→ clustering algorithm
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strength of the relation: 0.95 Audit 2026-09-28: DOUBTFUL - read against its span and kept, but subnetworks were revealed by a clustering algorithm; operationalised-as is loose.
concept_edges[0]the tagger's words
concept_edgesclaustrum —is-a→ hubs
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strength of the relation: 0.8 Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the span notes the claustrum's broad intracortical connections; is-a 'hubs' is inferred.
also in: claustrum · hubs
concept_edges[3]the tagger's words
concept_edgesmedial —distinct-from→ lateral
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strength of the relation: 0.9
also in: medial · lateral
concept_edges[5]the tagger's words
concept_edgeslateral entorhinal area —part-of→ trisynaptic circuit
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strength of the relation: 0.85 Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span writes 'ENTl'; the endpoint is a variant, and part-of is loose ('the starting point of' the circuit).
concept_edges[6]the tagger's words
content_tagscluster analysis
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content_tags.statistics[0]the tagger's words
content_tagspercentage agreement between two methods
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content_tags.statistics[1]the tagger's words
content_tagsweighted directional connectivity matrices
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content_tags.statistics[2]0.9the tagger's words
content_tagsclustering algorithm
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content_tags.statistics[3]1.0the tagger's words
content_tagssemi-quantitative densities
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content_tags.statistics[4]1.0the tagger's words
content_tagsThe mouse neocortex resolves into eight subnetworks: four somatic sensorimotor, two medial and two lateral, each with its own topology, communicating through selected cortical areas.
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content_tags.findings[0]the tagger's words
content_tagsAnterograde and retrograde tracing agreed on 89% of matrix entries, cross-validating the connectivity dataset.
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content_tags.findings[1]the tagger's words
content_tagsThe claustrum's cortical connectivity is asymmetric: it receives bilateral cortical input but sends output almost exclusively to the same hemisphere.
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content_tags.findings[2]the tagger's words
content_tagsThe temporal association, ectorhinal and perirhinal areas are back-labelled from layers 2 and 5a of the entire neocortex except ACAv, RSP and VISp.
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content_tags.findings[3]the tagger's words
content_tagsBecause every main node of the four somatic sensorimotor subnetworks is reciprocally connected, sensory and motor areas can interact directly without routing through higher-order association cortex.
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content_tags.findings[4]the tagger's words
content_tagsThe findings support cross-modal modulation, challenging the idea that mammalian primary sensory cortices are strictly unisensory.
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content_tags.findings[5]the tagger's words
content_tagsThe second medial subnetwork is a serial chain running from dorsal subiculum to RSPv to ACAv and then to the infralimbic, prelimbic and medial orbitofrontal areas.
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content_tags.findings[6]the tagger's words
content_tagsVentral retrosplenial cortex is the sole neocortical area receiving dense dorsal subicular input, making it the entry point for dorsal hippocampal information into neocortex.
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content_tags.findings[7]the tagger's words
content_tagsThe dorsolateral prefrontal cortex is where all four somatic sensorimotor subnetworks converge.
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content_tags.findings[8]the tagger's words
content_tagsThe ventromedial prefrontal cortex is where the medial and lateral subnetworks converge, letting external sensory and internal visceral/gustatory information be integrated.
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content_tags.findings[9]the tagger's words
content_tags89% of connections were labelled by both the anterograde and retrograde methods, so the two datasets largely agree
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content_tags.findings[10]1.0the tagger's words
content_tagsclustering placed every node into a small number of distinct cortico-cortical modules
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content_tags.findings[11]1.0the tagger's words
content_tagsthe four somatic sensorimotor modules each formed a separate subnetwork
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content_tags.findings[12]1.0the tagger's words
content_tagsthe claustrum and lateral entorhinal area have broad unique connections consistent with a hub role
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content_tags.findings[13]1.0the tagger's words
content_tagsclaustral connectivity is asymmetric: inputs bilateral, outputs almost exclusively ipsilateral
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content_tags.findings[14]1.0the tagger's words
content_tagsthe temporal subnetwork receives input from nearly the entire neocortex
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content_tags.findings[15]1.0the tagger's words
content_tagswithin the somatic sensorimotor subnetworks, sensory and motor areas interact directly without higher-order association areas
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content_tags.findings[16]1.0the tagger's words
content_tagsthe lateral subnetworks are points of massive convergence, each connected to a large number of cortical areas
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content_tags.findings[17]1.0the tagger's words
content_tagseach subnetwork converges onto a discrete territory of prefrontal cortex
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content_tags.findings[18]1.0the tagger's words
content_tagsthe prefrontal zones are relatively segregated, which may help define their unique processing roles
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content_tags.findings[19]1.0the tagger's words
content_tagsabout 600 pathways from around 317 co-injections are available, 304 efferent and 296 afferent
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content_tags.findings[20]1.0the tagger's words
content_tagsthe findings support cross-modal modulation, against strictly unisensory primary sensory cortices
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content_tags.findings[21]1.0the tagger's words
content_tagsmacro- or meso-connectome
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content_tags.definitions[0]the tagger's words
content_tagshub
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also in: hub
content_tags.definitions[1]the tagger's words
content_tagsiConnectome
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also in: iConnectome
content_tags.definitions[3]the tagger's words
content_tagsmeso-connectome
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content_tags.definitions[5]0.85the tagger's words
content_tagsdouble co-injection
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content_tags.definitions[6]1.0the tagger's words
content_tagshubs
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also in: hubs
content_tags.definitions[7]1.0the tagger's words
content_tagsclustering
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also in: clustering
content_tags.definitions[8]1.0the tagger's words
content_tagsintraconnectivity
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content_tags.definitions[9]the tagger's words
content_tagsinterconnectivity
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.definitions[10]the tagger's words
content_tagsinjection site
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.variables[0]the tagger's words
content_tagsdensity of intraconnectivity
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.variables[4]0.85the tagger's words
content_tagslaminar distribution patterns
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.variables[5]0.9the tagger's words
content_tagsanterograde and retrograde labeling
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.variables[6]1.0the tagger's words
content_tagsOver 600 — labelled neuronal pathways collected across the whole mouse neocortex
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[0]the tagger's words
content_tags240 — intracortical connections manually reconstructed into the common atlas frame
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[1]the tagger's words
content_tags89% — share of matrix entries labelled by both the anterograde and the retrograde method
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[2]the tagger's words
content_tags~600 pathways (304 efferent and 296 afferent), ~317 co-injections — contents of the released dataset at time of publication
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[3]the tagger's words
content_tags80 anterograde and 160 retrograde — pathways included in the reconstructed cortico-cortical connectivity map
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[4]the tagger's words
content_tags~ 250-500μm — diameter of the tracer co-injection sites
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[5]the tagger's words
content_tags50μm — section thickness used for all brains
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[6]the tagger's words
content_tagsover 600 labeled neuronal pathways — the atlas contents
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[7]1.0the tagger's words
content_tags240 — intracortical connections manually reconstructed into the common frame
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[8]1.0the tagger's words
content_tags89% — connections labelled by both tracer directions
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[9]1.0the tagger's words
content_tags~250-500μm — co-injection size, mostly confined within individual cortical areas
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[10]1.0the tagger's words
content_tags304 efferent and 296 afferent — pathway counts from about 317 co-injections
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[11]1.0the tagger's words
content_tags8 week old male C57Bl/6J mice — the animals
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.quantities[12]1.0the tagger's words

Interpretive choices

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