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q-bio.NC · Neurons and Cognitionanzsrc-for-2020: 320903

Thalamus-to-visual-cortex spike links in two Allen mouse Neuropixels data sets increase with tracer axon density only weakly; LP gives fewer links to V1 than to higher areas

Question: does mesoscale tracer axon density predict how often thalamic and visual-cortex units show fast directed spike links? Data: Allen Visual Coding Neuropixels (46 mice, 1,049,307 thalamus-cortex pairs) and Visual Behavior Neuropixels (69 mice, 768,943 pairs); LGd and LP units against units in six visual areas (V1, LM, RL, AL, PM, AM). A link is a cross-correlogram peak at +1 to +4 ms (thalamus leads) or -4 to -1 ms (cortex leads) above a hollow-Gaussian baseline. Anatomy: Allen tracer experiments; because many LP and LGd injections label both nuclei, the primary estimate used clean injections only. Result 1 (pre-specified, passed): with nucleus and area fixed effects, spike-count and cell-class controls, the odds of a thalamus-leading link increased 2.59 times (95% CI 1.58-4.24) and 1.92 times (1.47-2.52) per 10-fold density; route permutation p = 0.045 and 0.0013. Unmixed and all-injection tracer estimates, a sharp baseline, strict thresholds and different-probe pairs gave the same sign. The relation is compressed: density spans about 900-fold across the 12 routes, link rates about 10-fold. In Visual Coding a control lag (+21 to +24 ms) also had a slope (1.66), and the slope depended on the LGd-to-V1 route. Exploratory: LP projects more densely to V1 than to higher areas, but LP-to-V1 pairs had fewer links (odds ratio 0.49, 0.34-0.71; Visual Behavior 0.77, 0.53-1.10); LP-to-V1 axons end mostly in layers 1 and 5. LGd links preferred V1 only 2.6-4 times, against a 150-fold density ratio. Result 2 (pre-specified, failed): cortex-leading links did not follow area-to-thalamus density (1.40 and 1.14 per 10-fold, CIs include 1), stayed near control-lag rates, and came more from fast-spiking units, which do not project to the thalamus. Limitations: CCG links are putative; 12 routes give few degrees of freedom; tracer data come from other mice and few clean injections. Allen data are not bundled; code regenerates all derived tables.

thalamocortical · LGN · pulvinar · LP · visual cortex · higher visual areas · cross-correlogram · spike transmission · mesoscale connectome · tracer projection density · structure-function · corticothalamic · Neuropixels · Allen Brain Observatory · Visual Behavior Neuropixels · Allen Mouse Brain Connectivity Atlas · mouse · replication

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References

13
  1. usesdoi:10.1038/s41586-020-03171-x

    Source and description of the Allen Visual Coding Neuropixels data set.

  2. useshttps://portal.brain-map.org/circuits-behavior/visual-behavior-neuropixels

    Source of the Allen Visual Behavior Neuropixels data set used for replication.

  3. usesdoi:10.1038/nature13186

    Allen Mouse Brain Connectivity Atlas tracer experiments; source of projection densities.

  4. usesdoi:10.1038/s41586-019-1716-z

    Cre-line tracer experiments of the Allen connectivity atlas for thalamic and cortical injections.

  5. usesdoi:10.1162/netn_a_00066

    Knox 2019 voxel-model region matrix used as an alternative density estimate.

  6. usesdoi:10.1016/j.jneumeth.2008.12.029

    Hollow-Gaussian CCG baseline and detection method.

  7. doi:10.1016/j.neuron.2016.12.028

    LGN narrowband gamma rhythm that can add co-firing to CCGs.

  8. uses, supportsIn awake mice, putative LGN-to-V1 spike connections go mostly to fast-spiking layer 4 cells and follow retinotopy weakly, with no consistent ON/OFF rule, in two Allen Neuropixels data sets sci:sha256:2c36aa37a35ba7d53ad28506144bf2fef348a048bded50cf57ee1c874d3fc8af

    Source of the CCG detection rules and range-read code; our LGd-to-V1 layer 4 and fast-spiking preferences repeat its results.

  9. Axon projection density did not predict rate or direction of fast spike coupling between six mouse visual areas in two Allen Neuropixels data sets; target preference matched in one data set sci:sha256:1b49edfb4811d021f34cc9d60e81ad50df927eaeeb7426d2cb78d8a4676ada59

    Tracer density did not predict cortex-to-cortex fast spike links; we test thalamic routes with larger anatomical contrasts.

  10. Voxel-scale tracer projection density does not predict short-latency spike links between mouse visual areas better than distance in two Allen Neuropixels datasets sci:sha256:8652596e8108893e95c268255b4fd1d8779b572e76b1aee818940bff44dbae1b

    Voxel-scale tracer density versus cortex-to-cortex spike links in the same data sets.

  11. In 82 opto-tagged mouse visual cortex Neuropixels sessions, spike-train troughs confirmed rare Vip inhibition from slice data, but Sst-to-FS inhibition exceeded the slice prediction sci:sha256:cc2969a4538f2f63ba276e738d0e249095d66c05c612cfaf5c9cf3ba15f542dd

    In vivo class-specific connectivity from CCGs in the same Allen data sets.

  12. Local excitatory recurrence did not reliably predict stimulus-evoked Fano-factor quenching in 139 mice: visual cortex exceeded LGd/LP in Allen VCN but not VBN flashes, and CA3 equalled CA1 sci:sha256:6ea87a03ffd65472e95030d7a4287d8ffecd3df039d08f281ef3953e7928916a

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  13. https://alleninstitute.org/terms-of-use/

    Terms of the external Allen Institute data, which this bundle does not contain.

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