added more background rationale, stuff that can be integrated into main.txt intros.

README.md

@@ -7,19 +7,32 @@ The main manuscript file is **[wholeBrain_main.md][]**
 
 
 ## Rationale
-The idea is to provide a clear and beautiful representation of the visualized activity patterns in the developing brain.
+The idea is to provide a clear and beautiful representation of the visualized activity patterns within developing brain in vivo.
 
 ### Scientific importance
 A comprehensive description of the spatiotemporal activity patterns in the immature brain will be crucial to understanding the developmental dynamics that exist between intrinsic and extrinsic factors that regulate circuit development. 
 
 * signature patterns that predict current or future behavior
-* construction of self-organizing circuits (advanced robotics -- *Terminator, Skynet, Cylons*)
+* construction of self-organizing circuits (advanced robotics -- *Terminators, Skynet, & Cylons!*)
 
 ### Human health importance
 * neurodevelopmental disorders (autism, schizophrenia, epilepsy)
 * activity-dependent structural plasticity. Implications for brain repair.
 * development of brain-machine interfaces
 
+### Previous work 
+
+reference                           | FOV info                                                                                                                                                              | figure snapshot                                         
+----------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------  
+[Ackman et al][#Ackman:2012]        | 3 x 4 mm FOV WF-MCI in V1, V2, and SC P3-P9 mouse                                                                                                                     | ![](assets/img/Screen_Shot_2013-09-04_at_2.12.16_PM.png)
+[Siegel et al.][#Siegel:2012]       | 219x180 µm FOV 2P-MCI in visual cortex                                                                                                                               | ![](assets/img/Screen_Shot_2013-09-04_at_2.18.49_PM.png)
+[Chiu & Weliky][#Chiu:2001]         | linear MEA covering a 3.2 mm strip across visual cortex Corr activity observed between cortical patches separated by mean distance of 1 mm                            | ![](assets/img/Screen_Shot_2013-09-04_at_2.16.02_PM.png)
+[Colonnese et al.][#Colonnese:2010] | single pulled electrodes in V1 or linear MEA (16 site silcon probe, 4sites x 4shanks, with 200µm separation, 600µm total                                            | ![](assets/img/Screen_Shot_2013-09-04_at_1.54.43_PM.png)
+[Hanganu et al][#Hanganu:2006]      | single electrodes or 4 shank linear MEAs placed in each hemisphere (0.5-1.0mm spacing, for 1.5-3.0mm total)                                                           | ![](assets/img/Screen_Shot_2013-09-04_at_2.36.18_PM.png)
+[Yang et al][#Yang:2012a]           | 2.6 x 2.6 mm FOV, VSD imaging in S1 cortex P0-7 rat. Spont and evoked activity in C2 barrel. 8shank x 4site silicon probe linear MEA (200µm separation, 1.4mm total) | ![](assets/img/Screen_Shot_2013-09-04_at_2.26.32_PM.png)
+[Rochefort et al][#Rochefort:2009]  | 100x70µm FOV 2P-MCI in mouse visual cortex at P11                                                                                                                    | ![](assets/img/Screen_Shot_2013-09-04_at_2.47.37_PM.png)
+
+
 
 ### Future work 
 More detailed descriptions of the nature and the functions of these activity patterns can and should be performed in parallel in ongoing and future studies.  
@@ -44,7 +57,7 @@ Instructions for [converting multimarkdown to Word document][id4]
 
 Image processing and dataset generation will utilize custom code in the [wholeBrainDX] software project. 
 
-Datasets, and exploratory data analysis will use R code that lives inside this wholeBrain project repository. Datasets and raw data to big too be inside this git repo will be stored on external servers and linked to accordingly.
+Datasets and R code for exploratory data analysis and graphics will live inside this wholeBrain project repository. Datasets and raw data too big to be inside this git repo will be stored on external servers and linked to accordingly.
 
 
 [wholeBrain_main.md]: wholeBrain_main.md
@@ -56,3 +69,5 @@ Datasets, and exploratory data analysis will use R code that lives inside this w
 [id4]: https://gist.github.com/ackman678/6391902
 
 [wholeBrainDX]: https://github.com/ackman678/wholeBrainDX/blob/master/README.md  
+
+<<[references.txt]

references.txt

@@ -0,0 +1,243 @@
+# References #
+
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+
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+
+[#Xu:2011]: Xu, H.-p., Furman, M., Mineur, Y. S., Chen, H., King, S. L., Zenisek, D., Zhou, Z. J., Butts, D. A., Tian, N., Picciotto, M. R., and Crair, M. C. (2011).  An instructive role for patterned spontaneous retinal activity in mouse visual map development, Neuron, 70(6), 1115-27
+
+[#Zhang:2011]: Zhang, J., Ackman, J. B., Xu, H.-P., and Crair, M. C. (2011).  Visual map development depends on the temporal pattern of binocular activity in mice, Nat Neurosci, 15(2), 298-307
+
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+
+[#Cang:2013]: Cang, J. and Feldheim, D. A. (2013).  Developmental Mechanisms of Topographic Map Formation and Alignment, Annu Rev Neurosci, (),
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+[#Sarnaik:2013]: Sarnaik, R., Wang, B.-S., and Cang, J. (2013).  Experience-Dependent and Independent Binocular Correspondence of Receptive Field Subregions in Mouse Visual Cortex, Cereb Cortex, (),
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+
+[#Hooks:2006]: Hooks, B. M. and Chen, C. (2006).  Distinct roles for spontaneous and visual activity in remodeling of the retinogeniculate synapse, Neuron, 52(2), 281-91
+
+[#Stellwagen:2002]: Stellwagen, D. and Shatz, C. J. (2002).  An instructive role for retinal waves in the development of retinogeniculate connectivity, Neuron, 33(3), 357-367
+
+[#Sernagor:1995]: Sernagor, E. and Grzywacz, N. M. (1995).  Emergence of complex receptive field properties of ganglion cells in the developing turtle retina, J Neurophysiol, 73(4), 1355-64
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+
+[#Wong:1998]: Wong, W. T., Sanes, J. R., and Wong, R. O. (1998).  Developmentally regulated spontaneous activity in the embryonic chick retina, J Neurosci, 18(21), 8839-52
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+
+[#Chiu:2001]: Chiu, C. and Weliky, M. (2001).  Spontaneous activity in developing ferret visual cortex in vivo, J Neurosci, 21(22), 8906--8914
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+[#Tolonen:2007]: Tolonen, M., Palva, J. M., Andersson, S., and Vanhatalo, S. (2007).  Development of the spontaneous activity transients and ongoing cortical activity in human preterm babies, Neuroscience, 145(3), 997-1006
+
+[#Bansal:2000]: Bansal, A., Singer, J. H., Hwang, B. J., Xu, W., Beaudet, A., and Feller, M. B. (2000).  Mice lacking specific nicotinic acetylcholine receptor subunits exhibit dramatically altered spontaneous activity patterns and reveal a limited role for retinal waves in forming ON and OFF circuits in the inner retina, J Neurosci, 20(20), 7672-81
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+
+[#Cang:2013]: Cang, J. and Feldheim, D. A. (2013).  Developmental Mechanisms of Topographic Map Formation and Alignment, Annu Rev Neurosci, (), 
+
+[#Espinosa:2012]: Espinosa, J. S. and Stryker, M. P. (2012).  Development and plasticity of the primary visual cortex, Neuron, 75(2), 230-49
+
+[#Marder:2005]: Marder, E. and Rehm, K. J. (2005).  Development of central pattern generating circuits, Curr Opin Neurobiol, 15(1), 86-93
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+
+[#Maffei:1990]: Maffei, L. and Galli-Resta, L. (1990).  Correlation in the discharges of neighboring rat retinal ganglion cells during prenatal life, Proc Natl Acad Sci U S A, 87(7), 2861-2864
+
+[#Meister:1991]: Meister, M., Wong, R. O., Baylor, D. A., and Shatz, C. J. (1991).  Synchronous bursts of action potentials in ganglion cells of the developing mammalian retina, Science, 252(5008), 939-943
+
+[#Leinekugel:2002]: Leinekugel, X., Khazipov, R., Cannon, R., Hirase, H., Ben-Ari, Y., and Buzsáki, G. (2002).  Correlated bursts of activity in the neonatal hippocampus in vivo, Science, 296(5575), 2049-52
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+
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+
+[#Huberman:2003]: Huberman, A. D., Wang, G.-Y., Liets, L. C., Collins, O. A., Chapman, B., and Chalupa, L. M. (2003).  Eye-specific retinogeniculate segregation independent of normal neuronal activity, Science, 300(5621), 994--998
+
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+
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+[#Wang:2010b]: Wang, B.-S., Sarnaik, R., and Cang, J. (2010).  Critical period plasticity matches binocular orientation preference in the visual cortex, Neuron, 65(2), 246-56
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+[#Yang:2009]: Yang, J.-W., Hanganu-Opatz, I. L., Sun, J.-J., and Luhmann, H. J. (2009).  Three patterns of oscillatory activity differentially synchronize developing neocortical networks in vivo, J Neurosci, 29(28), 9011-25
+
+[#Olavarria:2003]: Olavarria, J. F. and Hiroi, R. (2003).  Retinal influences specify cortico-cortical maps by postnatal day six in rats and mice, J Comp Neurol, 459(2), 156-72
+
+[#Olavarria:2006]: Olavarria, J. F. and Safaeian, P. (2006).  Development of callosal topography in visual cortex of normal and enucleated rats, J Comp Neurol, 496(4), 495-512
+
+[#Ruthazer:2010a]: Ruthazer, E. S., Bachleda, A. R., and Olavarria, J. F. (2010).  Role of interstitial branching in the development of visual corticocortical connections: a time-lapse and fixed-tissue analysis, J Comp Neurol, 518(24), 4963-79
+
+[#Bock:2012]: Bock, A. S., Kroenke, C. D., Taber, E. N., and Olavarria, J. F. (2012).  Retinal input influences the size and corticocortical connectivity of visual cortex during postnatal development in the ferret, J Comp Neurol, 520(5), 914-32
+
+[#Laing:2012]: Laing, R. J., Bock, A. S., Lasiene, J., and Olavarria, J. F. (2012).  Role of retinal input on the development of striate-extrastriate patterns of connections in the rat, J Comp Neurol, 520(14), 3256-76
+
+
+
+
+
+
+[#Leamey:2009]: Leamey, C. A., Van Wart, A., and Sur, M. (2009).  Intrinsic patterning and experience-dependent mechanisms that generate eye-specific projections and binocular circuits in the visual pathway, Curr Opin Neurobiol, 19(2), 181-7
+
+[#Blankenship:2010]: Blankenship, A. G. and Feller, M. B. (2010).  Mechanisms underlying spontaneous patterned activity in developing neural circuits, Nat Rev Neurosci, 11(1), 18-29
+
+
+<!--- Standing waves, adult waves, pattern replay --->
+[#Benucci:2007]: Benucci, A., Frazor, R. A., and Carandini, M. (2007).  Standing waves and traveling waves distinguish two circuits in visual cortex, Neuron, 55(1), 103-17
+
+[#Han:2008]: Han, F., Caporale, N., and Dan, Y. (2008).  Reverberation of recent visual experience in spontaneous cortical waves, Neuron, 60(2), 321--327
+
+[#Lee:2002]: Lee, A. K. and Wilson, M. A. (2002).  Memory of sequential experience in the hippocampus during slow wave sleep, Neuron, 36(6), 1183-94
+
+
+
+
+<!--- More for wholeBrain paper 2013-09-04 14:33:53 --->
+[#Yang:2012a]: Yang, J.-W., An, S., Sun, J.-J., Reyes-Puerta, V., Kindler, J., Berger, T., Kilb, W., and Luhmann, H. J. (2012).  Thalamic Network Oscillations Synchronize Ontogenetic Columns in the Newborn Rat Barrel Cortex, Cereb Cortex, (), 
+
+[#Rochefort:2009]: Rochefort, N. L., Garaschuk, O., Milos, R.-I., Narushima, M., Marandi, N., Pichler, B., Kovalchuk, Y., and Konnerth, A. (2009).  Sparsification of neuronal activity in the visual cortex at eye-opening, Proc Natl Acad Sci U S A, 106(35), 15049-54
+
+
+
+
+

wholeBrain_main.md

@@ -34,3 +34,8 @@ The cerebral cortex exhibits spontaneous and sensory evoked patterns of activity
 
 <<[wholeBrain_results-hemisphere_corr.txt]
 
+
+# References
+
+<<[references.txt]
+