The cerebral cortex exhibits spontaneous and sensory evoked patterns of activity during fetal and postnatal development that are crucial for the activity-dependent formation and refinement of circuits [#Katz:1996]. Knowing the source and flow of these activity patterns locally and globally is crucial to understanding self-organization in the developing brain. Here we show that neural population activity within newborn mice in vivo is characterized by spatially discrete domains that are coordinated in a state dependent and areal dependent fashion throughout developing isocortex. Whole brain optical recordings from neonatal mice expressing a genetic calcium reporter showed that ongoing activity in the cerebral cortex was characterized by distinct and repetitively active domains measuring hundreds of microns in diameter. Domain activity exhibited mirror-symmetric patterns between the hemispheres, with strong correlations between specific portions of frontal and parietal cortex. Ongoing activity across the cortical hemispheres showed characteristic network architectures with a frontal-motor regions functionally connected to a parietal-sensory areas through secondary motor cortex, retrosplenial cortex, and posterior parietal cortex. Furthermore, ongoing cortical activity was regulated by physiological state with frontal cortex activity shifting from negative to positive correlations with motor behavior during the course of development. This study provides the first comprehensive description of population activity in the developing isocortex at a scope and scale that bridges the microscopic or macroscopic spatiotemporal resolutions provided by traditional neurophysiological or neuroimaging techniques. Mesoscale maps of cortical population dynamics within animal models will be vital to engineering future repair strategies and brain-machine interfaces for neurodevelopmental disorders.
Brain development requires neural activity and calcium dynamics for establishing proper circuit structure and function. The importance of neural activity in the prenatal and neonatal period can be easily recognized in children exposed to chemical agents affecting neurotransmission during the fetal period that result in severe brain malformations, epilepsy, and mental retardation. Indeed, embryonic limb movements in species ranging from chick to human are thought to be initiated by spontaneous motor neuron activity in the spinal cord and thought to be crucial for activity-dependent development of motor synapses [Schoenberg:2003] [Marder,Lichtmann]. However it is only recently that we have begun to appreciate the underlying patterns of persistent neural activity that in fact exist in the developing brain in vivo. For example, sensori-motor feedback associated with spontaneous movement generated by spinal motor neurons triggers synchronized 'spindle-burst' potentials among cells in somatosensory cortex [Yang:2009][Khazipov:2004a] before the start of locomotion and tactile behavior. Correlated bursts of activity occur in the developing rat hippocampus in vivo [#Leinekugel:2002] [Mohns&Blumberg]. Spontaneous retinal waves drive patterned activation of circuits throughout the immature visual system before the onset of vision [#Ackman:2012] [Hanganu,Colonnese?]. Furthermore, prenatal EEG recordings have demonstrated spindle burst oscillations and slow activity transients in the human infant somatosensory and occipital cortices before birth [#Vanhatalo:2005][#Tolonen:2007]. Nonetheless, a comprehensive account of the structural dynamics of persistent activity throughout the developing isocortex in vivo has not been undertaken.
Neocortical organization consists of cortical modules tiled across the cortical surface in a topographic fashion such that vertical arrays of cells concerned with specific sensory features are grouped together as columns [#Mountcastle:1997]. Most evidence to date suggests that columns/hyper/macro columns are 300-500µm diameter across species.
The patterns of activity that exist in the developing brain are unknown. We performed recordings from mice expressing the genetic calcium indicator GCaMP (gcamp3 or gcamp6) throughout cortical neurons. We performed our recordings in three age groups: P2-P5, P8-P9, and P12-13. We found that cortical activity was characterized by discrete domains of activation during the first two postnatal weeks. These activity domains ranged from 200-800 µm in diameter (*Ns*, *fig*), with larger sized domains of activation in the visual cortex and motor cortex (*Ns*, *fig*). In the second postnatal week the size of activations in the hindlimb/trunk representation was larger, The average duration of these domain activations was about 600 ms – 1 s (*Ns*, *fig*) with longer activations on the order of seconds to tens of seconds in visual cortex driven by retinal waves [#Ackman:2012].
We parcellated the brain into distinct anatomical boundaries by using reference coordinates from a mouse line that expressed the tdtomato reporter in thalamocortical afferents. The expression can be used to parcellate out areal boundearies of primary sensory cortical areas (wong riley 1979). We matched these parcellations to a Allen brain atlas adult mouse reference image and than linearly scaled the remaining parcellations in our FOV on to the images of our recordings that contain fucntional boundaries (like in the domain centroid activation plot and in the normalized domain frequency plots).
* Other slice calcium recordings, patch/gap junctions. In vivo physiology? (Not too many multisite electrode recordings in cortex, spatial resolution issue).
* Calcium imaging-- Konnerth 'waves' in Ent cortex [#Adelsberger:2005]. For visual cortex, domains activity in extrastriate cortex (Ackman Nature 2012). But S1-- [#Golshani:2009] work in later postnatal-- but activity not obeying domains in barrel cortex-- problem with spatial sampling in the xy and the z for this study?
To understand the patterns and how they interact we first looked at correlation between the hemispheres. Cortical activity exhibited high temporal cortelation between the hemispheres () . In additon this activity was highly correlated in the spatial dimension. For example epochs of time would exhibit high correlation in the medial-lateral dimension or in the rostral-caudal dimension. This strength of correlation temporally and spatially increased between the hemsipheres with a function of age.
<!--- * Each hemisphere 'training' the other one in preparation for behaviorally relevant sensory-motor imitations '[[mirror_neurons]]' hypothesis? --->
**Conclusions:** The two hemispheres seem to be mostly synchronized, though it’s possible the R hemispshere (which is also the slightly more ‘active’ hemisphere, see stats table below) leads the left by a bit. The asymmetric peak at –150–175frames is interesting. That would be about 30–35 sec.
The big secondary peaks around ±30 sec is present in both autocorrs and xcorrs and is far above the random normal xcorr baseline (blue trace). In fact there is a periodicity seen in the autocorrs and the xcorrs where there is a dampening oscillation about on this interval! (See ideal dampening frequency in random sine wave example above). This corresponds to a 1/30sec == 0.033 Hz ultra-slow oscillation.
{==Looking at the above plot showing lags from [–1000, 1000] frames which is ± 200 s, we can see about 5.5 cycles of this underlying dampening oscillation in both autocorr plots. This corresponds to (1000fr*0.2sec/fr)/5.5 => 36.36 sec/cycle => 0.0275 cycles/sec or ~0.03 Hz==}{>>Crazy!<<}
**Conclusions:** So the activity in both hemispheres at postnatal day 3 (P3) clearly exhibits significant spatial correlations in both in the medial-lateral and anterior-extent. This is consistent with and complementary to the fact that the active pixel fraction in each hemisphere exhibits a strong temporal correlation as I found earlier in this report [Temporal correlation of activity][]. The medial-lateral positional correlation is stronger than the anterior-posterior (higher *R* and lower *p* value). The total number of coactive frames is `numel(y1(~isnan(y1)&~isnan(y2)))` == **1114 frames**. This is accounts to **37.13%** of the movie or **222.8 s**. Cortex.L had 1635 actvFrames and cortex.R had 1677 actvFrames which means that each hemisphere was coactive with the other hemisphere 1114/1635 == **68.13%** and 1114/1677 == **66.43%** of the active time respectively.
* During anesthesia induction, there is rapid (<30 s) knock down of discrete domain activity (P3 mouse <120518_09.tif>). Cingulate, retrosplenial activations the last to go-- default mode/resting state network areas last.
Variation in the strength of correlation between cortical areas and the motor movement signal depended on brain region (p < 2.2e-16, anova) and age (p = 1.627e-05, anova) The first age group in which motor cortex exhibited signficant positive correlation with motor movements was at P12-13 (r=0.06±0.02, p-value = 0.001449, t-test).
## Developing cortical activity consists of distinct subnetworks
We then calculated a matrix of pearsons correlation coefficients based on the pixel active fraction timecourses for each pair of parcellations. The resulting assocaition matrix was run through a hierarchal clustering alogtithm to reveal functional modules of of activation. These functional modules typically consisted of 3 distinct subnetworks-- a frontal motor network, a posterior parietal network, a S1-body/limb network, and an auditory A1 network at P12.
We found many similarities but some striking differences as a function of age.
* **Ongoing activity in developing cortex is not random**-- specifically coordinated in space and time within and among cortical areas between the hemispheres
* created using area coords: 120518_07_2013-09-11-225029_d2rImageCoords20130930-144657.eps
* 120518_07_parcellation_fig.tif: alpha overlay of brightfield image with Allen gray parcellation image and Sert-tdtomato images linearly scaled to fit V1 & S1-barrel reprsentations in functional image and domain centroid map
* contourplot of 20 levels 120518_07_connComponents_BkgndSubtr-60px_noWatershed-20130327-151022_d2r_20130930-124942.eps
* activefraction hemis AP & ML all:  | 120518_07_connComponents_BkgndSubtr-60px_noWatershed-20130327-151022_d2ractiveFractionPixelLocaCorr20130423-094506.eps
* activefraction hemis AP & ML segment: 
* activefraction hemis AP & ML segment: 
### Cortical activity correlated between the hemispheres and is periodic
