manual merge mcc-->master
This commit is contained in:
ackman678
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## Supplementary Figure Legends
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**Supplmentary Figure 1.** **Subnetworks in developing isocortex.** **a** Areal trace examples. Synchronized activations between hemispheres indicated by red links.
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Supplementary Figure 1. Functional parcellation of developing neocortex. a, Image of tdtomato mouse brain at P7. Notice primary sensory areas outlined. b, Overlay of parcellations with Allen Brain atlas. c, Colored time projection of spontaneous activity in barrel cortex. d, Colored time projection overlay of functional mapping of somatosensory cortex with tactile stimulation.
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Supplementary Figure 2. Spatiotemporal properties of cortical domains. a, Boxplot distributions of cortical domain frequency by region. b, Relative cortical domain frequency, normalized to area. c, Mean and max signal intensity by cortical region.
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Extended Data Figure 3. Cortical domain activity exhibits bilateral symmetry. a Examples of domains exhibiting spatially symmetric activations. Notice most timepoints contain a mixture of symmetric and asymmetric domain activations. b Cortical active fraction timecourses for both hemispheres. c Hemispheric domain centers of mass for coactive frames in a recording along medial-lateral (ML) and anterior-posterior (AP) extents. Bottom left panels show the periods indicated by black bars at expanded view. Pearson's correlation: ML, r = 0.3241, p = 1.1591e-28; AP, r = 0.1479, p = 7.0982e-07. d Example temporal autocorrelation and cross-correlation functions for hemispheric cortical activity. Notice the peaks above gaussian distributed noise (blue traces). e Boxplots showing distribution of spatial and temporal correlation between the cortical hemispheres (P2–5, N = 22; P8–9, N = 30; P12–13, N = 38 movies).
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**supplementaryFig-symmetry.ai** **Cortical domain activity exhibits bilateral symmetry.** **a** Examples of domains exhibiting spatially symmetric activations. Notice most timepoints contain a mixture of symmetric and asymmetric domain activations. **b** Cortical active fraction timecourses for both hemispheres. **c** Hemispheric domain centers of mass for coactive frames in a recording along medial-lateral (ML) and anterior-posterior (AP) extents. Bottom left panels show the periods indicated by black bars at expanded view. Pearson's correlation: ML, p = 1.1591e-28; AP, p = 7.0982e-07. **d** Hemispheric autocorrelation and cross-correlation functions for cortical activity at all and short time lags. Notice the peaks above gaussian distributed noise (blue traces).
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Supplementary Figure 4. Cortical domain activity exhibits bilateral symmetry. a Examples of domains exhibiting spatially symmetric activations. Notice most timepoints contain a mixture of symmetric and asymmetric domain activations. b Cortical active fraction timecourses for both hemispheres. c Hemispheric domain centers of mass for coactive frames in a recording along medial-lateral (ML) and anterior-posterior (AP) extents. Bottom left panels show the periods indicated by black bars at expanded view. Pearson's correlation: ML, p = 1.1591e-28; AP, p = 7.0982e-07. d Hemispheric autocorrelation and cross-correlation functions for cortical activity at all and short time lags. Notice the peaks above gaussian distributed noise (blue traces).
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Supplementary Figure x. Cortical activity and physiological state. a, Active fraction rasters of cortical aactivity during isoflurane anesthesia at different ages. b, Pixel frequency maps during quiet and activty motor periods.
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#Figure Metadata
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<!--Figure 1 metadata
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* neonate_ms_fig.png
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* binary masks: Screen_Shot_2013-03-29_at_12.06.25_PM_crop.png, ..._crop1.png, ..._crop2.png
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* 133.6s timeColorMap projection: 120518_07-fr698-1365-20140710-222230.tif
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* Segmentation mask of 133.6s timeColorMap projection: 120518_07-fr698-1365-20140715-230320-cadj.png
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* parcellation map
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* update 2013-10-03 11:07:29:
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* 120518_07_2013-09-11-225029_d2rImageCoords20130930-144657.ai
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* created using area coords: 120518_07_2013-09-11-225029_d2rImageCoords20130930-144657.eps
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* 120518_07_parcellation_fig.tif: alpha overlay of brightfield image with Allen gray parcellation image and Sert-tdtomato images linearly scaled to fit V1 and S1-barrel reprsentations in functional image and domain centroid map
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* contourplot of 20 levels 120518_07_connComponents_BkgndSubtr-60px_noWatershed-20130327-151022_d2r_20130930-124942.eps
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* 120518_07_connComponents_BkgndSubtr-60px_noWatershed-20130327-151022_d2r_20130930-124950_eps.png
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* [x] add a domain centroid size/duration map similar to: 
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* 
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* domainFreq map: 20140613-084032_ActivityMapFigRawProj-domainFreqRdBu.eps, P5mapDomainFreq-crop.tif, P8mapDomainFreq-crop.tif, P13mapDomainFreq-crop.tif
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* domainFreq boxplot:
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* domainDur map: 20140613-082954_ActivityMapFigRawProj-domainDurRdBu.eps, P5mapDur-crop.tif, P8mapDur-crop.tif, P13mapDur-crop.tif
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* domainDur cdf:
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* domainDiam map: 20140613-083156_ActivityMapFigRawProj-domainDiamRdBu.eps, P5mapDiam-crop.tif, P8mapDiam-crop.tif, P13mapDiam-crop.tif
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* 2014-10-07 11:45:16 added cortex outlines to the diam map from:
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* 140328_outlines.ai
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* 140331_outlines.ai
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* 140509_outlines.ai
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-->
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<!-- Figure 2 metadata
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* Scatterplot mean freq: 140704-143614-freq_min-scatter.pdf
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* Scatterplot domain duration-diameter timeline: 140702-141423-durDiam-scatter-img.pdf
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* P3 M1 wave time projection, lomag: 140218_13-fr2564-2601-20140716-144024.tif
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* P5 V1 wave time projection, himag: 140328_10-fr2016-2153-20140710-092344.tif
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* P13 global wave time projection, lomag: ~~140509_07-fr1725-2004-20140717-172658.tif~~
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* P13 global wave time projection, lomag: 140509_22-fr484-609-20140725-155542.tif
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* wave motion index scatter: 140702-152109-rhoDiam-scatter.png
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* Wave motion index timeline: 140702-162029-waveMotionIdx-jitterTimeline.pdf
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-->
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<!--Figure 3 metadata
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* P8 isoflurane active px fraction and motor movement signal traces: 140331_11_20140425-171130_d2ractvFraction20140425-171354-20140425-171355.ai
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* P8 isoflurane time color projection sequence: 140331_11-fr775-975-20140710-163609.tif, 140331_11-fr1800-2000-20140710-162448.tif, 140331_11-fr2800-3000-20140710-162206.tif
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* Cortical and photodiode signals and moving averages color coded at diff lags: 120518_07_2013-09-11-225029_d2r_motorSignalFiltFilt_fig.eps
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~~* Pixel activation frequency map projections~~
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* quiet motor state: 120518_07_connComponents_BkgndSubtr-60px_noWatershed-20130327-151022_d2rActivityMapFigContour20131016-163945-20131023_MotorQuiet_eps.png
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* active motor state: 120518_07_connComponents_BkgndSubtr-60px_noWatershed-20130327-151022_d2rActivityMapFigContour20131016-163945-20131023_MotorActive_eps.png
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* xcorr traces for cortical activity and motor activity: 120518_07_20140604-151545_d2rmotorSignalXCorr20140604-152316.eps
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120518_07_20140604-151545_d2rmotorSignalXCorr20140604-152321.eps
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?* Time projection color maps, P5
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* 140328_09-fr514-536-20141003-143615-adj-merge.tif
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* 140328_09-fr1158-1174-20141003-144829-adj-merge.tif
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* 140328_09-fr2163-2231-20141003-145502-adj-merge.tif
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?* xcorr lags matrix for cortical activity and motor activity: motorXcorrLags_20140602-161719.eps
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* boxplot of zero lag corr coeff: 140602-205159-rvaluenode1-boxplot.pdf
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Figure 3. Cortical domain activity is state dependent.
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a, Experimental schematic. Red light illumination measured with a photodiode was used to monitor motor movements. b, Cortical activity (active pixel fraction by hemisphere) and motor movement signal after onset of isoflurane anesthesia at 205 s. c, Time projection maps (40 s segments) at times indicated in recording from b. d, Cortical activity and coincident motor movement activity signals. Active pixel fraction traces for motor (M1,M2), somatosensory (HL,FL,T; barrel), and visual (V1,V2) cortex shown at bottom of panel. e, Time projection map at P5 showing HL,FL,T and PPC activity coincident with motor movements. f, Mean cross-correlation functions between cortical regions and motor movement signals across all movies. Notice the high positive correlation between motor movement and S1-limb/body (HL,FL,T) signals at all ages. g, Boxplots of cortical activity and motor movement correlation at lag zero
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-->
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<!--Figure 4 metadata
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* corr matrix: MeanCorrMatrix-age-2014-06-02.ai, (140602-113013-age.g-groupCorrMatrix.pdf, 140602-112947-dendr-ageP12-13.pdf)
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* 140808-093608-graph-squaredEdgeScale-auto.pdf
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~~* corr graph spatial layout: 140602-100049-P12-13_0.15.pdf ~~
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-->
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<!--Figure 5 metadata
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* 140807-121720-graph-squaredEdgeScale.pdf
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~~* corr graph force layout: 140602-101610-P12-13_0.15.pdf~~
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~~140806-174912-modularity-boxplot.pdf~~
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~~140806-174917-diam-boxplot.pdf~~
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140806-174920-clusterCoeffGlobal-boxplot.pdf
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140806-174915-pathLength-boxplot.pdf
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* 140804-111208-eigCentr-scatterplot.pdf, r>0.15
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~~* 140804-075217-degree-hist.pdf, binwidth=2, r>0.15~~
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-->
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<!-- Supplementary Movies
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~~* SupplementaryMovie1-P3gcamp3.mov: wholeBrain-shortAlpha-lomed.mov, (120518_07.tif) 10 s long playback, 30fps, = 300fr = 60 s real time ~~
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2014-10-09 14:37:07
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* SupplementaryMovie1.mp4 P5, gcamp6, 180fr, 36 s real, 30fps, 6 s playback
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* 140328_gcamp6_P5-keyframe1-12000kbps.mp4 fr2821-3000 from 140328_06 20.4um/px for 11x13mm FOV
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~~* SupplementaryMovie2-P8gcamp3.mov:
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* 6 s long playback, 30fps, 6s*30fps+3fr = 184fr = 36.8 s real time
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~~* 131208_06_std_lomed-all.mov~~
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* 131208_06_std_med-all_340x240.mov
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2014-10-09 14:37:03
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* SupplementaryMovie2.mp4
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140331_06-gcamp6-P8-12000kbps.mp4 fr, 180 fr from 1/3 through. Nice SC.R wave 20.4 um/px for 11x13 FOV
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2014-10-09 14:37:11
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* SupplmentaryMovie3.mp4
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* 140404_03-gcamp6-P12 1.mp4 27.2 um/px * 540px for 14x17mm FOV
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~~* SupplementaryMovie3-P13gcamp6.mov: ~~
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* 10 s long playback, 30fps, 9*30+18 = 288 = 57.6s real time.
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~~* 140509_21_288fr_med_al_transl_340x240-2.mov~~
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~~* 140509_21-fr1-3000-20140908-101333-dFoF.avi, 288fr near beginning of movie after first movements and during whisking and second movements.~~
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* 140509_21_286fr_medhi_al_transl_340x240-2.mov 2.4MB
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* 140509_21-fr1-900-20140908-131010-dFoF.avi, New dF/F (shorter baseline avg) and scaled to reduce movement vessel. 286fr near beginning of movie after first movements and during whisking and second movements.
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* 140509_21-trans3-medhigh.mov, from 140509_21-trans3 (based on 140509-trans2 from above) 2.3MB, 320x240, 9:16, 10s, 286fr, about 3/4 through 140509_21-fr1-900-20140908-131010-dFoF.avi
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* SupplementaryMovie4-P13gcamp6.mov:
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* 8 s long playback, 30fps, 8*30+11fr=. 50.2 s real time.
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~~* 140509_22_fr484-735-lo-all-trans.mov~~
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* 140509_22_fr484-735-med-all-trans_340x240.mov
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* SupplementaryMovie5-P8gcamp6-isofl.mov
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~~140331_11-isofl_fr873-1697_h264_lo_all_crop_340x240.mov~~
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* SupplementaryMovie-isofl-P8gcamp6.mov: 140331_11-isofl-trans3.mov, lo, 5.4MB 44 s duration, 249 s total recording time
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* 285s total recording length, 6x playback, 30fps
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* 140331_11-fr1-3000-20140904-234725-dFoF.avi, fr 873 - 1697 = 165 s
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~~* 140331_12-fr1-3000-20140907-111217-dFoF.avi, fr 2400 - 3000 = 120 s~~
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* 140331_12-fr1-3000-20140907-111217-dFoF.avi, fr 1 - 402 = 84 s
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2014-10-09 16:11:54
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* SupplementaryMovie5.mp4
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* 140331_11-isofl-trans3 1 4512.mp4
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* SupplementaryMovie6-P13gcamp6-isofl.mov
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* 140509_30-isofl-trans2-adj2.mov, lomed, 6x playback, 30fps, 4.4MB, 44 s duration, 249 s total recording time
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* 140509_30-fr1-3000-20140924-105444-dFoF.avi, fr 873 - 1697 = 165 s
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* 140509_31-fr1-3000-20140924-113131-dFoF.avi, fr 1 - 402 = 84 s
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2014-10-09 16:11:02
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* SupplementaryMovie6.mp4
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* 140509_30-isofl-trans2 1 4512kbps.mp4
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-->
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<!-- Supplementary Figs
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* SupplementaryFig1.ai Functional parcellation of developing neocortex.
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* Data/confocal/Chelsea/120625/07_0.3x_SertTdTomato_P5_8bit_crop.tif
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* Parcellation outlines: 140224_01_dummyAreaOutlines.tif & Rhemi Illustrator outlines in Fig. 1d
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* Allen brain ref image, cropped from darkest version in: 120518_07_parcellation_fig.tif
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* Barrel crop SERT-tdtomato image: 08_0.3x_SertTdTomato_P5_crop_Lbarrels2.tif
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* Time projection map of barrels: 120221_02-fr360-3000-20140902-130321.tif
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TODO: d, Colored time projection overlay of functional mapping of somatosensory cortex with tactile stimulation.
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* SupplementaryFig2.ai
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* supplementaryFig-areal-stats.ai:
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* 140702-204319-freq_min-boxplot.pdf
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* 140703-083800-freq_min-boxplot.pdf
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* 140606-091326-diamnodeT-boxplot.png
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* 140606-091332-MeanIntensitynodeT-boxplot.png
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* 140606-091338-MaxIntensitynodeT-boxplot.png
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* 140606-091345-Duration_snodeT-boxplot.png
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* 140606-143236-pairwisetPvalMatrix.pdf
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* SupplementaryFig3.ai
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* supplementaryFig-symmetry.ai:
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* binary mask snapshots, cropped from screen shots in [[2013-04-19_analysis]]
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* Screen_Shot_2013-04-19_at_8.26.00_AM_fr1786.png
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* Screen_Shot_2013-04-19_at_8.27.49_AM_fr2134.png
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* Screen_Shot_2013-04-19_at_8.30.27_AM_fr759.png
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* Screen_Shot_2013-04-19_at_8.30.51_AM_fr373.png
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* Screen_Shot_2013-04-19_at_8.38.54_AM_fr177.png
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* Temporal correlation of activity between the hemispheres and preceding motor activation:
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* 
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* hemisphere active fraction traces: Screen_Shot_2013-04-08_at_8.47.19_AM.png
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* activefraction hemis AP and ML all:  | 120518_07_connComponents_BkgndSubtr-60px_noWatershed-20130327-151022_d2ractiveFractionPixelLocaCorr20130423-094506.eps
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* activefraction hemis AP and ML segment: 
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* activefraction hemis AP and ML segment: 
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### Cortical activity correlated between the hemispheres and is periodic
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* hemi auto and xcorr:
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* 2500fr lags: 120518_07_connComponents_BkgndSubtr-60px_noWatershed-20130327-151022activeFraction20130408-143100.eps
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* 250fr lags: 120518_07_connComponents_BkgndSubtr-60px_noWatershed-20130327-151022activeFraction20130408-151655.eps
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* 1500fr lags: 120518_07_2013-10-18_AllgoodactiveFraction20131023-145023.eps
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* SupplementaryFig4.ai
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* 141022-141235-smallworldness-boxplot.pdf
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* supplementaryFig-montage.ai:
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* 140509_22-fr484-735-20140729-102651-montage.png, 140509_22-fr484-735-20140729-102651-montage.tif
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* supplementaryFig-corticaltracesCorr.ai:
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* P5: 140328_10_20140420-111218_d2rActvRaster20140420-111804.eps, 3000fr
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* P8: 140331_05_20140425-160657_d2rActvRaster20140425-161244.eps, 3000fr
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* P13: 140509_22_20140522-074327_d2rActvRaster20140522-075627.eps, 3000fr
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-->
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