wholeBrain/README.md

# wholeBrain imaging paper

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][]**



## Rationale
The idea is to provide a clear and beautiful representation of the visualized activity patterns in the developing brain.

### 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*)

### Human health importance
* neurodevelopmental disorders (autism, schizophrenia, epilepsy)
* activity-dependent structural plasticity. Implications for brain repair.
* development of brain-machine interfaces


### 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.  
For example:  
 
* What is the intra- vs sub- cortical nature of barrel cortex activity (E.M.'s work)
* What is the intra- vs sub- cortical nature of ongoing activity in motor- associational-, and other non-primary sensory cortical areas?
* Relationship of imaged patterns to EEG patterns described in other studies?
* Extent to which functional correlations reflect direct synaptic connections?
* Retinal wave drive of other areas?
* Ontogenetic relationships of localized calcium domains?
* Development profile through first postnatal weeks
* Chronic developmental profile in individuals?
* Aberrant activity patterns in developmental disorder and seizure models?


## Workflow

Writing 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]

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.


[wholeBrain_main.md]: wholeBrain_main.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

[wholeBrainDX]: https://github.com/ackman678/wholeBrainDX/blob/master/README.md