jackman/wholeBrain
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Edits to abstr, intro, fig3 legend in main.md

Browse Source
This commit is contained in:
ackman678
2013-09-17 13:52:44 -04:00
parent 1c3b778c22
commit 7c5e6e295c
2 changed files with 38 additions and 13 deletions
Download Patch File Download Diff File Expand all files Collapse all files

31
analysis/120518_07_2013-09-11-225029_d2r-wholeBrain_activeFraction.txt Normal file
View File

@@ -0,0 +1,31 @@
name actvFraction maxFraction minFraction meanFraction sdFraction meanActvFraction sdActvFraction actvFrames actvTimeFraction nonActvFrames nonActvTimeFraction
cortex.L 0.94462 0.11391 0 0.011953 0.018076 0.021933 0.019512 1635 0.545 1365 0.455
cortex.R 0.98936 0.1788 0 0.011325 0.019276 0.02026 0.021993 1677 0.559 1323 0.441
V1.L 0.91092 0.49268 0 0.01166 0.048811 0.085525 0.10573 409 0.13633 2591 0.86367
V1.R 1 0.49303 0 0.01563 0.049954 0.082406 0.087538 569 0.18967 2431 0.81033
V2M.R 1 0.53362 0 0.010531 0.047479 0.10746 0.11235 294 0.098 2706 0.902
V2M.L 0.99889 0.72727 0 0.015069 0.070498 0.15535 0.17184 291 0.097 2709 0.903
V2L.R 0.99979 0.83261 0 0.0093884 0.051119 0.10279 0.13809 274 0.091333 2726 0.90867
V2L.L 0.89476 0.47959 0 0.011748 0.048174 0.10396 0.10477 339 0.113 2661 0.887
A1.L 0.94332 0.81434 0 0.0056521 0.038994 0.14745 0.13751 115 0.038333 2885 0.96167
A1.R 0.89896 0.51003 0 0.0032766 0.029558 0.12287 0.13523 80 0.026667 2920 0.97333
barrel.L 1 0.48431 0 0.014222 0.051387 0.10432 0.099942 409 0.13633 2591 0.86367
barrel.R 1 0.48833 0 0.014424 0.050157 0.10278 0.094128 421 0.14033 2579 0.85967
AS.L 1 0.61732 0 0.017578 0.063066 0.13626 0.12119 387 0.129 2613 0.871
AS.R 1 0.72344 0 0.016043 0.064496 0.14073 0.13779 342 0.114 2658 0.886
PPC.L 1 0.52809 0 0.013443 0.050858 0.11425 0.10241 353 0.11767 2647 0.88233
PPC.R 0.99316 0.51777 0 0.0085395 0.043173 0.11698 0.11357 219 0.073 2781 0.927
LS.L 1 0.73378 0 0.011153 0.061789 0.18904 0.17674 177 0.059 2823 0.941
LS.R 1 0.88002 0 0.0092979 0.060153 0.19371 0.19978 144 0.048 2856 0.952
FL.L 1 0.83896 0 0.013279 0.073959 0.21888 0.21303 182 0.060667 2818 0.93933
FL.R 1 0.70978 0 0.013078 0.059922 0.16766 0.14208 234 0.078 2766 0.922
HL.L 1 1 0 0.02413 0.10457 0.28726 0.23402 252 0.084 2748 0.916
HL.R 1 0.96645 0 0.019074 0.098036 0.26614 0.26196 215 0.071667 2785 0.92833
T.L 1 0.7411 0 0.017038 0.070106 0.15825 0.15284 323 0.10767 2677 0.89233
T.R 1 0.47762 0 0.0091402 0.042031 0.10587 0.10127 259 0.086333 2741 0.91367
RSA.L 0.99984 0.85963 0 0.021561 0.083406 0.18272 0.17196 354 0.118 2646 0.882
RSA.R 1 0.52748 0 0.01318 0.053458 0.10572 0.11474 374 0.12467 2626 0.87533
M1.L 0.99877 0.30664 0 0.012884 0.037771 0.071976 0.061002 537 0.179 2463 0.821
M1.R 0.99979 0.38526 0 0.013534 0.039764 0.063539 0.065195 639 0.213 2361 0.787
M2.L 0.90863 0.3212 0 0.0067742 0.026208 0.050934 0.054044 399 0.133 2601 0.867
M2.R 0.99698 0.293 0 0.011429 0.035556 0.070262 0.060359 488 0.16267 2512 0.83733

20
wholeBrain_main.md
View File

@@ -8,7 +8,7 @@ Mesoscale mapping of neural activity across developing cerebral hemispheres
# 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 [#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 discrete and repetitively active domains measuring hundreds of microns in diameter. Cortical domain activity depended on brain state with periods of localized and global domain synchrony exhibiting positive and negative correlations to motor behavior respectively. Furthermore, domain activity exhibited mirror-symmetric patterns between the hemispheres, with strong correlations between cortical areas that correspond to the default-mode network in primates. 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.
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. Cortical domain activity depended on brain state with periods of localized and global domain synchrony exhibiting positive and negative correlations to motor behavior respectively. Furthermore, domain activity exhibited mirror-symmetric patterns between the hemispheres, with strong correlations between cortical areas that correspond to the default-mode network in primates. 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.
@@ -17,7 +17,7 @@ The cerebral cortex exhibits spontaneous and sensory evoked patterns of activity
<!--- This should be one paragraph. Some of this intro material could be combined with intro or concl sentences in abstract for a Nature letter (should be referenced and up to 300 words; 200 words preferred) --->
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 has been recognized in chick to human and is 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 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]. However, a comprehensive account of the structural dynamics of persistent activity throughout the developing isocortex in vivo has not been undertaken.
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 is 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 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]. However, a comprehensive account of the structural dynamics of persistent activity throughout the developing isocortex in vivo has not been undertaken.
- Neural activity, drugs, and birth defects
@@ -37,7 +37,7 @@ Brain development requires neural activity and calcium dynamics for establishing
# Results
## Ongoing activity in the developing cerebral cortex is characterized by discrete domains
## Ongoing activity in developing isocortex is characterized by discrete domains
* Cortical column (mini/meso/super columns) history (20th century anatomists-- sherrington, valverde, rakic, etc).
* Column physiology-- Hubel and Wiesel. Rodent V1?
@@ -53,7 +53,7 @@ Brain development requires neural activity and calcium dynamics for establishing
metric | mean | min | max | unit
------------- | ----- | ---- | ------ | --------------------
diameter | 396.0 | 22.7 | 2383.5 | µm
diameter | 396.0 | 22.7 | 2383.5 | µm
duration | 0.6 | 0.2 | 14.6 | s
frequency | 2.9 | | | domains/sec/hemisphere
[**Table 1: Domain statistics**]
@@ -111,15 +111,7 @@ lenActvFraction>0 | fracCorr | timeCorr_s | fracCorrPos | timeCorrPos_s | fracCo
<!--- * Each hemisphere 'training' the other one in preparation for behaviorally relevant sensory-motor imitations '[[mirror_neurons]]' hypothesis? --->
![**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** Hemispheric domain centers of mass for coactive frames in a recording along medial-lateral (ML) and anterior-posterior (AP) extents. Bottom panels show the periods indicated by black bars at expanded view. **c** Plot of hemispheric domain centers of mass for coactive frames. **d** Correlation matrix of domain activity among cortical areas.](figure3.png)
xy pearson corr coef ML | xy pearson corr coef AP
--- | ---
p = 1.1591e-28 | p = 7.0982e-07
*scatterplots in figure 3* ||
![**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** 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. **c** Correlation matrix of domain activity among cortical areas.](figure3.png)
@@ -130,6 +122,8 @@ p = 1.1591e-28 | p = 7.0982e-07
<!--- # References --->
<<[references.txt]
<!--- # Metadata --->
<!---Figure 1 metadata
* neonate_ms_fig.png
* binary masks: Screen_Shot_2013-03-29_at_12.06.25_PM_crop.png, ..._crop1.png, ..._crop2.png