# Structured population activity across developing neocortex
# Abstract
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. Knowing the source and flow of these activity patterns locally and globally is crucial to understanding self-organization in the developing brain. Here we describe a system for imaging patterns of activity throughout the developing neocortex at the 'mesoscopic' level of resolution in transgenic mice expressing the genetic calcium indicator GCaMP3. Ongoing activity in the neonatal cerebral cortex was characterized by discrete and repetitively active domains measuring 100s of microns in diameter. This technique offers an unprecedented ability to study functional connectivity within and between the cerebral hemispheres at a scope and scale which bridges the microscopic or macroscopic resolutions offered by traditional neurophysiology and neuroimaging (fMRI) based recordings and will provide a practical means to assess cortical connectivity with high spatial resolution in pathophysiological models for autism, epilepsy, and schizophrenia.
- is the activity completely random? Or Is it organized in space and time, and at what scale?
- the little that we know is from work in second postnatal week, not earlier, olavarria work, interneuon migration, synaptic formation, and anatomical studies indicates significant development decisions are being made in first postnatal week
* 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?
* What about ongoing activity in other cortical areas during early brain development? Surgical procedure relevance.
* No population calcium activity found during gen'l anesthesia, only slow traveling waves.
* During anesthesia induction, 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.
<120518_09_mjpeg.mov>
### Cortical activity and motor activity is periodic
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
### Cortical activity is correlated with the motor signal
**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.
