added to readme and removed extra files from parts branch

README.md

@@ -1,6 +1,28 @@
 # wholeBrain imaging paper
 
-The goal of this work is to provide a general description of the population activity patterns that occur in developing cerebral cortex.
+The goal of this work is to provide a broad description of the population activity patterns that occur in developing cerebral cortex.
 
-The main manuscript file is [[wholeBrain_main.md]]
+The main manuscript file is [wholeBrain_main.md][]
 
+## Rationale
+
+The idea is to provide a clear and beautiful visualization of the immature activity patterns in the developing brain.
+
+We can do this because
+
+## Workflow
+
+Workflow will be similar to that used previously for [current opinion review][id3]. Some useful info in [currOpinRvw outline][id2].
+
+Instructions for [converting multimarkdown to Word document][id4]
+
+
+
+
+[wholeBrain_main.md]: whole_brain.md
+
+[id2]: https://github.com/ackman678/currOpinRvw/blob/master/currOpin_outline.md  
+
+[id3]: https://github.com/ackman678/currOpinRvw/blob/master/README.md 
+
+[id4]: https://gist.github.com/ackman678/6391902

wholeBrain_abstr-2013-05-13.txt

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-# 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.

wholeBrain_abstr-current.txt

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-<<[wholeBrain_abstr-2013-05-13.txt]

wholeBrain_index.txt

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-Author: James B. Ackman  
-Date: 2012-12-31 12:30:49  
-Date Modified: 2013-05-13 13:30:03  
-Tags: paper, draft, manuscript, literature, research, retinal waves, Spontaneous Activity, development  
-
-<<[wholeBrain_title-current.txt]
-
-<<[wholeBrain_abstr-current.txt]
-
-<<[wholeBrain_intro-current.txt]
-
-<<[wholeBrain_results-current.txt]

wholeBrain_intro-current.txt

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-<<[wholeBrain_intro_2013-05-13.txt]

wholeBrain_intro_2013-05-13.txt

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-# Introduction  
-
-- Activity and development
-- Neural activity, drugs, and birth defects
-	- epilepsy
-	- autism
-- What is the activity?
-     - instructive or permissive?
-     - EEG slow oscillations not detectable until P10 in rodent.
-     - slice work
-     - leinekukel and khazipov work
-     - ucla konnerth imaging work
-     - human occipital cortex and my retinal wave paper
-     - 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
-

wholeBrain_results-current.txt

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-# Results
-
-<<[wholeBrain_results-ongoing_activity.txt]
-
-<<[wholeBrain_results-state_dependence.txt]
-
-<<[wholeBrain_results-hemisphere_corr.txt]
-

wholeBrain_title-current.txt

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-# Structured population activity across developing neocortex